1
|
Condello V, Roberts JW, Stenman A, Larsson C, Viswanathan K, Juhlin CC. Atrophic changes in thyroid tumors are strong indicators of underlying DICER1 mutations: a bi-institutional genotype-phenotype correlation study. Virchows Arch 2024:10.1007/s00428-024-03802-y. [PMID: 38637342 DOI: 10.1007/s00428-024-03802-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 03/26/2024] [Accepted: 04/05/2024] [Indexed: 04/20/2024]
Abstract
Somatic and biallelic DICER1 mutations are reported in subsets of thyroid tumors, supporting the role of this gene in thyroid tumor development. As recent studies have brought attention to macrofollicular patterns, atrophic changes, and papillary structures as being associated with DICER1 mutations, we sought to explore these observations in a bi-institutional cohort. A total of 61 thyroid lesions (54 tumors and 7 cases of thyroid follicular nodular disease; TFND), including 26 DICER1 mutated and 35 DICER1 wildtype controls were subjected to histological re-investigation and clinical follow-up. DICER1-mutated lesions showed a statistically significant association with younger age at surgery (29.2 ± 12.5 versus 51.3 ± 18.8, p = 0.0001), a predominant macrofollicular growth pattern (20/26 mutated cases versus 18/35 wildtype; p = 0.01) and atrophic changes (20/26 mutated cases versus 2/35 wildtype; p = 0.0001). Similar results were obtained when excluding TFND cases. We also present clinical and histological triaging criteria for DICER1 sequencing of thyroid lesions, which led to the identification of DICER1 variants in 16 out of 26 cases (62%) when followed. Among these, 3 out of 12 cases with available data were found to carry a constitutional DICER1 mutation. This observation suggests that the majority of DICER1 mutations are somatic-however implies that sequencing of constitutional tissues could be clinically motivated. We conclude that DICER1 mutations are amassed in younger patients with macrofollicular-patterned tumors and, most strikingly, atrophic changes. Given the rate of constitutional involvement, our findings could be of clinical value, allowing the pathologist to triage cases for genetic testing based on histological findings.
Collapse
Affiliation(s)
- Vincenzo Condello
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden.
| | - James W Roberts
- Department of Pathology and Laboratory Medicine, Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Adam Stenman
- Department of Breast, Endocrine Tumors and Sarcoma, Karolinska University Hospital, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Catharina Larsson
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Kartik Viswanathan
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Winship Cancer Center, Decatur, GA, USA
| | - C Christofer Juhlin
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden.
- Department of Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden.
| |
Collapse
|
2
|
Kong D, Wu Y, Liu Q, Huang C, Wang T, Huang Z, Gao Y, Li Y, Guo H. Functional analysis and validation of oncodrive gene AP3S1 in ovarian cancer through filtering of mutation data from whole-exome sequencing. Eur J Med Res 2024; 29:231. [PMID: 38609993 PMCID: PMC11015698 DOI: 10.1186/s40001-024-01814-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
BACKGROUND High-grade serous ovarian carcinoma (HGSOC) is the most aggressive and prevalent subtype of ovarian cancer and accounts for a significant portion of ovarian cancer-related deaths worldwide. Despite advancements in cancer treatment, the overall survival rate for HGSOC patients remains low, thus highlighting the urgent need for a deeper understanding of the molecular mechanisms driving tumorigenesis and for identifying potential therapeutic targets. Whole-exome sequencing (WES) has emerged as a powerful tool for identifying somatic mutations and alterations across the entire exome, thus providing valuable insights into the genetic drivers and molecular pathways underlying cancer development and progression. METHODS Via the analysis of whole-exome sequencing results of tumor samples from 90 ovarian cancer patients, we compared the mutational landscape of ovarian cancer patients with that of TCGA patients to identify similarities and differences. The sequencing data were subjected to bioinformatics analysis to explore tumor driver genes and their functional roles. Furthermore, we conducted basic medical experiments to validate the results obtained from the bioinformatics analysis. RESULTS Whole-exome sequencing revealed the mutational profile of HGSOC, including BRCA1, BRCA2 and TP53 mutations. AP3S1 emerged as the most weighted tumor driver gene. Further analysis of AP3S1 mutations and expression demonstrated their associations with patient survival and the tumor immune response. AP3S1 knockdown experiments in ovarian cancer cells demonstrated its regulatory role in tumor cell migration and invasion through the TGF-β/SMAD pathway. CONCLUSION This comprehensive analysis of somatic mutations in HGSOC provides insight into potential therapeutic targets and molecular pathways for targeted interventions. AP3S1 was identified as being a key player in tumor immunity and prognosis, thus providing new perspectives for personalized treatment strategies. The findings of this study contribute to the understanding of HGSOC pathogenesis and provide a foundation for improved outcomes in patients with this aggressive disease.
Collapse
Affiliation(s)
- Deshui Kong
- Department of Obstetrics and Gynecology, Peking University Third Hospital, No.49 Huayuanbei Rd., Haidian District, Beijing, 100191, People's Republic of China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital), Beijing, China
| | - Yu Wu
- Department of Obstetrics and Gynecology, Peking University Third Hospital, No.49 Huayuanbei Rd., Haidian District, Beijing, 100191, People's Republic of China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital), Beijing, China
| | - Qiyu Liu
- Department of Obstetrics and Gynecology, Peking University Third Hospital, No.49 Huayuanbei Rd., Haidian District, Beijing, 100191, People's Republic of China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital), Beijing, China
| | - Cuiyu Huang
- Department of Obstetrics and Gynecology, Peking University Third Hospital, No.49 Huayuanbei Rd., Haidian District, Beijing, 100191, People's Republic of China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital), Beijing, China
| | - Tongxia Wang
- Department of Obstetrics and Gynecology, Peking University Third Hospital, No.49 Huayuanbei Rd., Haidian District, Beijing, 100191, People's Republic of China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital), Beijing, China
| | - Zongyao Huang
- Department of Obstetrics and Gynecology, Peking University Third Hospital, No.49 Huayuanbei Rd., Haidian District, Beijing, 100191, People's Republic of China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital), Beijing, China
| | - Yan Gao
- Department of Obstetrics and Gynecology, Peking University Third Hospital, No.49 Huayuanbei Rd., Haidian District, Beijing, 100191, People's Republic of China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital), Beijing, China
| | - Yuan Li
- Department of Obstetrics and Gynecology, Peking University Third Hospital, No.49 Huayuanbei Rd., Haidian District, Beijing, 100191, People's Republic of China.
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital), Beijing, China.
| | - Hongyan Guo
- Department of Obstetrics and Gynecology, Peking University Third Hospital, No.49 Huayuanbei Rd., Haidian District, Beijing, 100191, People's Republic of China.
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital), Beijing, China.
| |
Collapse
|
3
|
White B, Swietach P. What can we learn about acid-base transporters in cancer from studying somatic mutations in their genes? Pflugers Arch 2024; 476:673-688. [PMID: 37999800 PMCID: PMC11006749 DOI: 10.1007/s00424-023-02876-y] [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: 09/25/2023] [Revised: 10/24/2023] [Accepted: 10/30/2023] [Indexed: 11/25/2023]
Abstract
Acidosis is a chemical signature of the tumour microenvironment that challenges intracellular pH homeostasis. The orchestrated activity of acid-base transporters of the solute-linked carrier (SLC) family is critical for removing the end-products of fermentative metabolism (lactate/H+) and maintaining a favourably alkaline cytoplasm. Given the critical role of pH homeostasis in enabling cellular activities, mutations in relevant SLC genes may impact the oncogenic process, emerging as negatively or positively selected, or as driver or passenger mutations. To address this, we performed a pan-cancer analysis of The Cancer Genome Atlas simple nucleotide variation data for acid/base-transporting SLCs (ABT-SLCs). Somatic mutation patterns of monocarboxylate transporters (MCTs) were consistent with their proposed essentiality in facilitating lactate/H+ efflux. Among all cancers, tumours of uterine corpus endometrial cancer carried more ABT-SLC somatic mutations than expected from median tumour mutation burden. Among these, somatic mutations in SLC4A3 had features consistent with meaningful consequences on cellular fitness. Definitive evidence for ABT-SLCs as 'cancer essential' or 'driver genes' will have to consider microenvironmental context in genomic sequencing because bulk approaches are insensitive to pH heterogeneity within tumours. Moreover, genomic analyses must be validated with phenotypic outcomes (i.e. SLC-carried flux) to appreciate the opportunities for targeting acid-base transport in cancers.
Collapse
Affiliation(s)
- Bobby White
- Department of Physiology, Anatomy and Genetics, University of Oxford, Parks Road, Oxford, OX1 3PT, UK.
| | - Pawel Swietach
- Department of Physiology, Anatomy and Genetics, University of Oxford, Parks Road, Oxford, OX1 3PT, UK
| |
Collapse
|
4
|
Zeisbrich M, Schindler V, Krausz M, Proietti M, Mrovecova P, Voll RE, Glaser C, Röther F, Warnatz K, Venhoff N. [Macrocytic anemia and polychondritis: VEXAS syndrome]. Z Rheumatol 2024; 83:229-233. [PMID: 36735069 PMCID: PMC10973061 DOI: 10.1007/s00393-023-01318-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/23/2022] [Indexed: 02/04/2023]
Abstract
An adult-onset autoinflammatory syndrome caused by somatic mutations in the UBA1 gene on the X chromosome was first reported in 2020. This VEXAS syndrome (acronym for vacuoles, E1 enzyme, X‑linked, autoinflammatory, somatic) is characterized by an overlap of rheumatic inflammatory diseases with separate hematologic abnormalities. A substantial number of affected patients suffer from treatment refractory relapsing polychondritis and nearly always show signs of macrocytic anemia. This case report illustrates the diagnostic key points to recognizing patients with VEXAS syndrome.
Collapse
Affiliation(s)
- Markus Zeisbrich
- Klinik für Rheumatologie und Klinische Immunologie, Vaskulitis-Zentrum Freiburg, Universitätsklinikum Freiburg, Medizinische Fakultät, Albert-Ludwigs-Universität Freiburg, Freiburg, Deutschland.
- Klinik für Rheumatologie und Klinische Immunologie, Universitätsklinikum Freiburg, Hugstetter Str. 55, 79106, Freiburg, Deutschland.
| | - Viktoria Schindler
- Klinik für Rheumatologie und Klinische Immunologie, Vaskulitis-Zentrum Freiburg, Universitätsklinikum Freiburg, Medizinische Fakultät, Albert-Ludwigs-Universität Freiburg, Freiburg, Deutschland
| | - Máté Krausz
- Centrum für chronische Immundefizienz, Universitätsklinikum Freiburg, Medizinische Fakultät, Albert-Ludwigs-Universität Freiburg, Freiburg, Deutschland
- Biologische Fakultät, Albert-Ludwigs-Universität Freiburg, Freiburg, Deutschland
| | - Michele Proietti
- Centrum für chronische Immundefizienz, Universitätsklinikum Freiburg, Medizinische Fakultät, Albert-Ludwigs-Universität Freiburg, Freiburg, Deutschland
| | - Pavla Mrovecova
- Centrum für chronische Immundefizienz, Universitätsklinikum Freiburg, Medizinische Fakultät, Albert-Ludwigs-Universität Freiburg, Freiburg, Deutschland
| | - Reinhard E Voll
- Klinik für Rheumatologie und Klinische Immunologie, Vaskulitis-Zentrum Freiburg, Universitätsklinikum Freiburg, Medizinische Fakultät, Albert-Ludwigs-Universität Freiburg, Freiburg, Deutschland
| | - Cornelia Glaser
- Klinik für Rheumatologie und Klinische Immunologie, Vaskulitis-Zentrum Freiburg, Universitätsklinikum Freiburg, Medizinische Fakultät, Albert-Ludwigs-Universität Freiburg, Freiburg, Deutschland
| | - Fabian Röther
- Praxis für Rheumatologie in Donaueschingen, Sonnenhaldenstr. 2, 78166, Donaueschingen, Deutschland
| | - Klaus Warnatz
- Klinik für Rheumatologie und Klinische Immunologie, Vaskulitis-Zentrum Freiburg, Universitätsklinikum Freiburg, Medizinische Fakultät, Albert-Ludwigs-Universität Freiburg, Freiburg, Deutschland
- Centrum für chronische Immundefizienz, Universitätsklinikum Freiburg, Medizinische Fakultät, Albert-Ludwigs-Universität Freiburg, Freiburg, Deutschland
| | - Nils Venhoff
- Klinik für Rheumatologie und Klinische Immunologie, Vaskulitis-Zentrum Freiburg, Universitätsklinikum Freiburg, Medizinische Fakultät, Albert-Ludwigs-Universität Freiburg, Freiburg, Deutschland
- Klinik für Rheumatologie und Klinische Immunologie, Universitätsklinikum Freiburg, Hugstetter Str. 55, 79106, Freiburg, Deutschland
| |
Collapse
|
5
|
Ren P, Zhang J, Vijg J. Somatic mutations in aging and disease. GeroScience 2024:10.1007/s11357-024-01113-3. [PMID: 38488948 DOI: 10.1007/s11357-024-01113-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 02/27/2024] [Indexed: 03/17/2024] Open
Abstract
Time always leaves its mark, and our genome is no exception. Mutations in the genome of somatic cells were first hypothesized to be the cause of aging in the 1950s, shortly after the molecular structure of DNA had been described. Somatic mutation theories of aging are based on the fact that mutations in DNA as the ultimate template for all cellular functions are irreversible. However, it took until the 1990s to develop the methods to test if DNA mutations accumulate with age in different organs and tissues and estimate the severity of the problem. By now, numerous studies have documented the accumulation of somatic mutations with age in normal cells and tissues of mice, humans, and other animals, showing clock-like mutational signatures that provide information on the underlying causes of the mutations. In this review, we will first briefly discuss the recent advances in next-generation sequencing that now allow quantitative analysis of somatic mutations. Second, we will provide evidence that the mutation rate differs between cell types, with a focus on differences between germline and somatic mutation rate. Third, we will discuss somatic mutational signatures as measures of aging, environmental exposure, and activities of DNA repair processes. Fourth, we will explain the concept of clonally amplified somatic mutations, with a focus on clonal hematopoiesis. Fifth, we will briefly discuss somatic mutations in the transcriptome and in our other genome, i.e., the genome of mitochondria. We will end with a brief discussion of a possible causal contribution of somatic mutations to the aging process.
Collapse
Affiliation(s)
- Peijun Ren
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Jie Zhang
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jan Vijg
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
| |
Collapse
|
6
|
Cho SF, Yeh TJ, Wang HC, Du JS, Gau YC, Lin YY, Chuang TM, Liu YC, Hsiao HH, Moi SH. Prognostic mutation signature would serve as a potential prognostic predictor in patients with diffuse large B-cell lymphoma. Sci Rep 2024; 14:6161. [PMID: 38485750 PMCID: PMC10940711 DOI: 10.1038/s41598-024-56583-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 03/08/2024] [Indexed: 03/18/2024] Open
Abstract
The present study aimed to elucidate the prognostic mutation signature (PMS) associated with long-term survival in a diffuse large B-cell lymphoma (DLBCL) cohort. All data including derivation and validation cohorts were retrospectively retrieved from The Cancer Genome Atlas (TCGA) database and whole-exome sequencing (WES) data. The Lasso Cox regression analysis was used to construct the PMS based on WES data, and the PMS was determined using the area under the receiver operating curve (AUC). The predictive performance of eligible PMS was analyzed by time-dependent receiver operating curve (ROC) analyses. After the initial evaluation, a PMS composed of 94 PFS-related genes was constructed. Notably, this constructed PMS accurately predicted the 12-, 36-, and 60-month PFS, with AUC values of 0.982, 0.983, and 0.987, respectively. A higher level of PMS was closely linked to a significantly worse PFS, regardless of the molecular subtype. Further evaluation by forest plot revealed incorporation of international prognostic index or tumor mutational burden into PMS increased the prediction capability for PFS. The drug-gene interaction and pathway exploration revealed the PFS-related genes were associated with DNA damage, TP53, apoptosis, and immune cell functions. In conclusion, this study utilizing a high throughput genetic approach demonstrated that the PMS could serve as a prognostic predictor in DLBCL patients. Furthermore, the identification of the key signaling pathways for disease progression also provides information for further investigation to gain more insight into novel drug-resistant mechanisms.
Collapse
Affiliation(s)
- Shih-Feng Cho
- Division of Hematology & Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
- Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
- Center for Cancer Research, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
- Center for Liquid Biopsy and Cohort Research, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
| | - Tsung-Jang Yeh
- Division of Hematology & Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
- Center for Cancer Research, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
| | - Hui-Ching Wang
- Division of Hematology & Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
| | - Jeng-Shiun Du
- Division of Hematology & Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
| | - Yuh-Ching Gau
- Division of Hematology & Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
| | - Yu-Yin Lin
- Health Management Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
| | - Tzer-Ming Chuang
- Division of Hematology & Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
| | - Yi-Chang Liu
- Division of Hematology & Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
| | - Hui-Hua Hsiao
- Division of Hematology & Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
| | - Sin-Hua Moi
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, 807, Taiwan.
- Research Center for Precision Environmental Medicine, Kaohsiung Medical University, Kaohsiung, 807, Taiwan.
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, 807, Taiwan.
| |
Collapse
|
7
|
Terré A, Vautier M, Kahn JE, Georgin-Lavialle S, Boursier G. Efficacy of canakinumab for mosaic tumor necrosis factor receptor associated periodic syndrome. Eur J Intern Med 2024:S0953-6205(24)00041-4. [PMID: 38307733 DOI: 10.1016/j.ejim.2024.01.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/22/2024] [Accepted: 01/25/2024] [Indexed: 02/04/2024]
Affiliation(s)
- Alexandre Terré
- Department of Internal Medicine, Sorbonne University, AP-HP, Tenon hospital, Centre de référence des maladies auto-inflammatoires et des amyloses d'origine inflammatoire (CEREMAIA), 20, rue de la Chine, GRC-28, Paris 75020, France
| | - Mathieu Vautier
- Department of Internal Medicine and Clinical Immunology France, AP-HP, Hôpital Pitié Salpetrière, Centre national de référence maladies Autoimmunes Systémiques rares, Centre national de référence maladies Autoinflammatoires et Amylose, and Inflammation-Immunopathology-Biotherapy Department (DMU i3), Sorbonne Universités, Paris, France
| | - Jean-Emmanuel Kahn
- Department of Internal Medicine, Paris Saclay University, AP-HP, Ambroise Paré Hospital, Boulogne Billancourt, France
| | - Sophie Georgin-Lavialle
- Department of Internal Medicine, Sorbonne University, AP-HP, Tenon hospital, Centre de référence des maladies auto-inflammatoires et des amyloses d'origine inflammatoire (CEREMAIA), 20, rue de la Chine, GRC-28, Paris 75020, France.
| | - Guilaine Boursier
- Laboratoire de Génétique des Maladies rares et autoinflammatoires, Service de Génétique moléculaire et cytogénomique, CHU Montpellier, Univ Montpellier, CeRéMAIA, Montpellier, France
| |
Collapse
|
8
|
Terré A, Magnotti F, Piot JM, Boursier G, Georgin-Lavialle S. Pyrin-associated autoinflammatory disease with p.Thr577Ala MEFV somatic mutation. Eur J Intern Med 2024; 120:139-141. [PMID: 37981528 DOI: 10.1016/j.ejim.2023.11.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/05/2023] [Accepted: 11/08/2023] [Indexed: 11/21/2023]
Affiliation(s)
- Alexandre Terré
- Sorbonne University, AP-HP, Tenon hospital, Department of Internal Medicine, Centre de référence des maladies auto-inflammatoires et des amyloses d'origine inflammatoire (CEREMAIA), GRC-28, Paris, France
| | - Flora Magnotti
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, LYON, France
| | - Jean-Maxime Piot
- Service de Rhumatologie, Centre Hospitalier du Mans, le Mans, France
| | - Guilaine Boursier
- Laboratoire de Génétique des Maladies rares et autoinflammatoires, Service de Génétique moléculaire et cytogénomique, CHU Montpellier, Univ Montpellier, CeRéMAIA, Montpellier, France
| | - Sophie Georgin-Lavialle
- Sorbonne University, AP-HP, Tenon hospital, Department of Internal Medicine, Centre de référence des maladies auto-inflammatoires et des amyloses d'origine inflammatoire (CEREMAIA), GRC-28, Paris, France.
| |
Collapse
|
9
|
Han X, Jia X, Sheng C, Li M, Han J, Duan F, Wang K. A comparison analysis of the somatic mutations in early-onset gastric cancer and traditional gastric cancer. Clin Res Hepatol Gastroenterol 2024; 48:102287. [PMID: 38253255 DOI: 10.1016/j.clinre.2024.102287] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 01/19/2024] [Accepted: 01/20/2024] [Indexed: 01/24/2024]
Abstract
BACKGROUND Early onset gastric cancer (EOGC) has been on the rise in recent years and differs slightly in pathology from traditional gastric cancer (TGC). Somatic mutations have an essential role in the development of gastric cancer. We aimed to investigate these two types of gastric cancers at the level of somatic mutations and to further understanding of gastric cancer development. METHODS Somatic mutation, copy number variation (CNV), and clinical information were obtained from TCGA and UCSC Xena. Samples were divided into EOGC (< 50 years old, N = 28) and TGC (≥ 50 years old, N = 395) groups based on age. R packages "maftools" and "sigminer" were used to identify mutation signatures, while CNV information was processed using GISTIC2.0. RESULTS CDH1(21 %, P = 0.030) and ARID1A (28 %, P = 0.014) were more common in EOGC and TGC, respectively. The mutation frequency of ARID1A increased with age, while the opposite was true for CDH1. Sex, Lauren classifications, tumor mutation burden levels, mutation status of TP53, MUC6, NIPBL, KRAS, and copy number variation of the WOOX can affect the activity of the mutant signature. CONCLUSIONS Early-onset gastric cancer and traditional gastric cancer have distinct somatic mutation signatures, each with its own relatively specific high-frequency mutated genes, and the gene's mutation frequency correlates with age. Several clinical factors and genetic status affect the activity of some mutational features in gastric cancer in both groups.
Collapse
Affiliation(s)
- Xiaoxuan Han
- College of Public Health, Zhengzhou University, Zhengzhou, Henan Province, China; Key Laboratory of Tumor Epidemiology of Henan Province, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, Henan Province, China
- College of Public Health, Zhengzhou University, Zhengzhou, Henan Province, China; Key Laboratory of Tumor Epidemiology of Henan Province, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, Henan Province, China.
| | - Xiaoxiao Jia
- College of Public Health, Zhengzhou University, Zhengzhou, Henan Province, China; Key Laboratory of Tumor Epidemiology of Henan Province, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, Henan Province, China
- College of Public Health, Zhengzhou University, Zhengzhou, Henan Province, China; Key Laboratory of Tumor Epidemiology of Henan Province, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, Henan Province, China.
| | - Chong Sheng
- College of Public Health, Zhengzhou University, Zhengzhou, Henan Province, China; Key Laboratory of Tumor Epidemiology of Henan Province, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, Henan Province, China
- College of Public Health, Zhengzhou University, Zhengzhou, Henan Province, China; Key Laboratory of Tumor Epidemiology of Henan Province, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, Henan Province, China.
| | - Mengyuan Li
- College of Public Health, Zhengzhou University, Zhengzhou, Henan Province, China; Key Laboratory of Tumor Epidemiology of Henan Province, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, Henan Province, China
- College of Public Health, Zhengzhou University, Zhengzhou, Henan Province, China; Key Laboratory of Tumor Epidemiology of Henan Province, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, Henan Province, China.
| | - Jinxi Han
- College of Public Health, Zhengzhou University, Zhengzhou, Henan Province, China; Key Laboratory of Tumor Epidemiology of Henan Province, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, Henan Province, China
- College of Public Health, Zhengzhou University, Zhengzhou, Henan Province, China; Key Laboratory of Tumor Epidemiology of Henan Province, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, Henan Province, China.
| | - Fujiao Duan
- College of Public Health, Zhengzhou University, Zhengzhou, Henan Province, China; Key Laboratory of Tumor Epidemiology of Henan Province, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, Henan Province, China
- College of Public Health, Zhengzhou University, Zhengzhou, Henan Province, China; Key Laboratory of Tumor Epidemiology of Henan Province, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, Henan Province, China.
| | - Kaijuan Wang
- College of Public Health, Zhengzhou University, Zhengzhou, Henan Province, China; Key Laboratory of Tumor Epidemiology of Henan Province, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, Henan Province, China
- College of Public Health, Zhengzhou University, Zhengzhou, Henan Province, China; Key Laboratory of Tumor Epidemiology of Henan Province, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, Henan Province, China.
| |
Collapse
|
10
|
Ariffin NS. Increased RUNX1 mutations in breast cancer disease progression. Pathol Res Pract 2024; 254:155076. [PMID: 38219493 DOI: 10.1016/j.prp.2023.155076] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/29/2023] [Accepted: 12/30/2023] [Indexed: 01/16/2024]
Abstract
Despite advances in screening, therapy and surveillance, breast cancer remains threatening to women. Worst, patients suffer from side effects of treatments and cancer cells become resistant. The emergence of RUNX1 in breast cancer has put it in a spotlight due to its roles in the disease progression. It also plays important roles in normal mammary glands such as for cell growth, proliferation, migration and stemness. However, mutations in the RUNX1 gene have changed the regulation of these phenotypes and the full spectrum of its implications in breast cancer patients is unknown. In this study therefore, the pattern of RUNX1 mutations in breast cancer patients was examined to understand its fundamental impacts on the disease. The perturbation of RUNX1 and its mutations in breast cancer was elucidated through different studies reported in cBioPortal in the past ten years. From our analyses, the majority of RUNX1 mutations were found in the primary breast cancer, with women constituted most of the mutations, especially on the left side of the breast. Similarly, increased number of mutations was observed in ER-positive breast cancer patients and this was also the case at the early stage of the disease development. The level of RUNX1 mutations also increased gradually as patients got older and the peak was highest in the patients of 60-70 years old. Altogether, these data indicated that the mutated RUNX1 gene contributed to the progression of breast cancer and understanding of its regulatory mechanisms is crucial to therapeutically target this gene in the future.
Collapse
Affiliation(s)
- Nur Syamimi Ariffin
- Department of Pharmacology and Pharmaceutical Chemistry, Faculty of Pharmacy, Universiti Teknologi MARA, 42300 Bandar Puncak Alam, Selangor, Malaysia.
| |
Collapse
|
11
|
Chai Y, Ma Y, Feng W, Xiang H, Lu H, Jin L. Identification and validation of a 4-extracellular matrix gene signature associated with prognosis and immune infiltration in lung adenocarcinoma. Heliyon 2024; 10:e24162. [PMID: 38293522 PMCID: PMC10827462 DOI: 10.1016/j.heliyon.2024.e24162] [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: 07/27/2023] [Revised: 11/27/2023] [Accepted: 01/04/2024] [Indexed: 02/01/2024] Open
Abstract
Background The extracellular matrix (ECM) plays a crucial role in the development and tumor microenvironment of lung adenocarcinoma (LUAD). This study aimed to establish a risk score of ECM-related genes in LUAD and explore the association between the risk score and patient survival as well as immune cell infiltration, somatic mutations, and therapy response. Methods Gene expression data from The Cancer Genome Atlas (TGCA) and eight Gene Expression Omnibus (GEO) databases were used to analyze and identify differentially expressed genes (DEGs). Prognostic ECM-related genes were identified and utilized to formulate a prognostic signature. A nomogram was constructed using TCGA dataset and validated in two GEO datasets. Differences between high- and low-risk patients were analyzed for function enrichment, immune cell infiltration, somatic mutations, and therapy response. Finally, Quantitative real-time PCR (qRT-PCR) was used to detect the mRNA expression of DEGs in LUAD. Results A risk score based on four ECM-related genes, ANOS1, CD36, COL11A1, and HMMR, was identified as an independent prognostic factor for overall survival (OS) compared to other clinical variables. Subsequently, a nomogram incorporating the risk score and TNM staging was developed using the TCGA dataset. Internal and external validation of the nomogram, conducted through calibration plots, C-index, time-dependent receiver operating characteristics (ROC), integrated discrimination improvement (IDI), and decision curve analyses (DCA), demonstrated the excellent discriminatory ability and clinical practicability of this nomogram. The risk score correlated with the distribution of function enrichment, immune cell infiltration, and immune checkpoint expression. More somatic mutations occurred in the high-risk group. The risk score also demonstrated a favorable ability to predict immunotherapy response and drug sensitivity. Conclusion A novel signature based on four ECM-related genes is developed to help predict LUAD prognosis. This signature correlates with tumor immune microenvironment and can predict the response to different therapies in LUAD patients.
Collapse
Affiliation(s)
- Yanfei Chai
- Department of Health Management Center, The Third Xiangya Hospital of Central South University, Changsha, China
- Department of Cardiothoracic Surgery, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Yuchao Ma
- Department of Cardiothoracic Surgery, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Wei Feng
- Department of Cardiothoracic Surgery, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Hong Xiang
- Department of Health Management Center, The Third Xiangya Hospital of Central South University, Changsha, China
- Center for Experimental Medicine, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Hongwei Lu
- Department of Health Management Center, The Third Xiangya Hospital of Central South University, Changsha, China
- Center for Experimental Medicine, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Longyu Jin
- Department of Cardiothoracic Surgery, The Third Xiangya Hospital of Central South University, Changsha, China
| |
Collapse
|
12
|
Bai M, Jiang N, Fu W, Huang C, Tian L, Mi N, Gao L, Ma H, Lu Y, Cao J, Zhang C, Yue P, Zhang Y, Lin Y, Meng W, Li X. Establishment and characterization of a novel hilar cholangiocarcinoma cell line, CBC3T-1. Hum Cell 2024; 37:364-375. [PMID: 37966669 PMCID: PMC10764469 DOI: 10.1007/s13577-023-01003-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 10/24/2023] [Indexed: 11/16/2023]
Abstract
Cholangiocarcinoma (CCA) is a group of malignant heterogeneous cancer arising from the biliary tree. The tumor is characterized by insidious onset, high degree of malignancy, poor prognosis, and high recurrence rate. Immortalized cancer cell lines are the best and easiest models for in vitro cancer research. Here, we established a naturally immortalized highly tumorigenic hilar cholangiocarcinoma (hCCA) cell line, CBC3T-1. The CBC3T-1 cell line was cultured for over 60 passages. Thorough analysis showed that CBC3T-1 cells share characteristics similar to original tumor cells from patients with cholangiocarcinoma and display a stable phenotype, including features of epithelial origin, stem cell-like properties, as well as a high invasive and migratory capability and tumorigenicity in mice. Furthermore, this cell line showed the best sensitivity to paclitaxel, followed by gemcitabine. RNA sequencing and whole‑exome sequencing showed that cancer-associated pathways and somatic mutations played a dominant role in the development of CCA. We established and characterized a new hCCA cell line, CBC3T-1, which contributes to a better understanding of bile duct cancer, and can be used to study tumorigenesis and progression and the role of anticancer drugs.
Collapse
Affiliation(s)
- Mingzhen Bai
- The First Clinical Medical College of Lanzhou University, Lanzhou, 730030, Gansu, China
| | - Ningzu Jiang
- The First Clinical Medical College of Lanzhou University, Lanzhou, 730030, Gansu, China
| | - Wenkang Fu
- The First Clinical Medical College of Lanzhou University, Lanzhou, 730030, Gansu, China
| | - Chongfei Huang
- The First Clinical Medical College of Lanzhou University, Lanzhou, 730030, Gansu, China
| | - Liang Tian
- The First Clinical Medical College of Lanzhou University, Lanzhou, 730030, Gansu, China
| | - Ningning Mi
- The First Clinical Medical College of Lanzhou University, Lanzhou, 730030, Gansu, China
| | - Long Gao
- The First Clinical Medical College of Lanzhou University, Lanzhou, 730030, Gansu, China
| | - Haidong Ma
- The First Clinical Medical College of Lanzhou University, Lanzhou, 730030, Gansu, China
| | - Yawen Lu
- The First Clinical Medical College of Lanzhou University, Lanzhou, 730030, Gansu, China
| | - Jie Cao
- The First Clinical Medical College of Lanzhou University, Lanzhou, 730030, Gansu, China
| | - Chao Zhang
- The First Clinical Medical College of Lanzhou University, Lanzhou, 730030, Gansu, China
| | - Ping Yue
- The First Clinical Medical College of Lanzhou University, Lanzhou, 730030, Gansu, China
- Department of General Surgery, The First Hospital of Lanzhou University, Lanzhou, 730030, Gansu, China
| | - Yong Zhang
- Department of General Surgery, The First Hospital of Lanzhou University, Lanzhou, 730030, Gansu, China
| | - Yanyan Lin
- Department of General Surgery, The First Hospital of Lanzhou University, Lanzhou, 730030, Gansu, China.
| | - Wenbo Meng
- Department of General Surgery, The First Hospital of Lanzhou University, Lanzhou, 730030, Gansu, China.
- Gansu Province Key Laboratory of Biological Therapy and Regenerative Medicine Transformation, Lanzhou, 730030, Gansu, China.
| | - Xun Li
- Department of General Surgery, The First Hospital of Lanzhou University, Lanzhou, 730030, Gansu, China
- Gansu Province Key Laboratory of Biological Therapy and Regenerative Medicine Transformation, Lanzhou, 730030, Gansu, China
| |
Collapse
|
13
|
Liu HL, Peng H, Huang CH, Zhou HY, Ge J. Mutational separation and clinical outcomes of TP53 and CDH1 in gastric cancer. World J Gastrointest Surg 2023; 15:2855-2865. [PMID: 38222005 PMCID: PMC10784822 DOI: 10.4240/wjgs.v15.i12.2855] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/18/2023] [Accepted: 11/21/2023] [Indexed: 12/27/2023] Open
Abstract
BACKGROUND Gastric cancer (GC) is a deadly tumor with the fifth highest occurrence and highest global mortality rates. Owing to its heterogeneity, the underlying mechanism of GC remains unclear, and chemotherapy offers little benefit to individuals. AIM To investigate the clinical outcomes of TP53 and CDH1 mutations in GC. METHODS In this study, 202 gastric adenocarcinoma tumor tissues and their corresponding normal tissues were collected. A total of 490 genes were identified using target capture. Through t-test and Wilcoxon rank-sum test, somatic mutations, microsatellite instability, and clinical statistics, including overall survival, were detected, compared, and calculated. RESULTS The mutation rates of 32 genes, including TP53, SPEN, FAT1, and CDH1 exceeded 10%. TP53 mutations had a slightly lower overall occurrence rate (33%). The TP53 mutation rate was significantly higher in advanced stages (stage III/IV) than that in early stages (stage I/II) (P < 0.05). In contrast, CDH1 mutations were significantly associated with diffuse GC. TP53 is related to poor prognosis of advanced-stage tumors; nevertheless, CDH1 corresponds to a diffuse type of cancer. TP53 is exclusively mutated in CDH1 and is primarily affected by two distinct GC mechanisms. CONCLUSION Different somatic mutation patterns in TP53 and CDH1 indicate two major mechanisms of GC.
Collapse
Affiliation(s)
- He-Li Liu
- Department of Gastrointestinal Surgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, China
| | - Huan Peng
- Clinical Nursing Teaching and Research Section, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, China
| | - Chang-Hao Huang
- Teaching and Research Section of Clinical Nursing, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, China
| | - Hai-Yan Zhou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, China
| | - Jie Ge
- Department of Gastrointestinal Surgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, China
| |
Collapse
|
14
|
Su D, Xiong Y, Wang S, Wei H, Ke J, Li H, Wang T, Zuo Y, Yang L. Structural deep clustering network for stratification of breast cancer patients through integration of somatic mutation profiles. Comput Methods Programs Biomed 2023; 242:107808. [PMID: 37716222 DOI: 10.1016/j.cmpb.2023.107808] [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] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/15/2023] [Accepted: 09/10/2023] [Indexed: 09/18/2023]
Abstract
BACKGROUND AND OBJECTIVE Breast cancer is among of the most malignant tumor that occurs in women and is one of the leading causes of death from gynecologic malignancy worldwide. The high degree of heterogeneity that characterizes breast cancer makes it challenging to devise effective therapeutic strategies. Accumulating evidence highlights the crucial role of stratifying breast cancer patients into clinically significant subtypes to achieve better prognoses and treatments. The structural deep clustering network is a graph convolutional network-based clustering algorithm that integrates structural information and has achieved state-of-the-art performance in various applications. METHODS In this study, we employed structural deep clustering network to integrate somatic mutation profiles for stratifying 2526 breast cancer patients from the Memorial Sloan Kettering Cancer Center into two clinically differentiable subtypes. RESULTS Breast cancer patients in cluster 1 exhibited better prognosis than breast cancer patients in cluster 2, and the difference between them was statistically significant. The immunogenomic landscape further demonstrated that cluster 1 was associated with remarkable infiltration of the tumor infiltrating lymphocytes. The clustering subtype could be used to evaluate the therapeutic benefit of immunotherapy and chemotherapy in breast cancer patients. Furthermore, our approach effectively classified patients from eight different cancer types, demonstrating its generalizability. CONCLUSIONS Our study represents a step towards a generic methodology for classifying cancer patients using only somatic mutation data and structural deep clustering network approaches. Employing structural deep clustering network to identify breast cancer subtypes is promising and can inform the development of more accurate and personalized therapies.
Collapse
Affiliation(s)
- Dongqing Su
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Yuqiang Xiong
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Shiyuan Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Haodong Wei
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Jiawei Ke
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Honghao Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Tao Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Yongchun Zuo
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China; Digital College, Inner Mongolia Intelligent Union Big Data Academy, Inner Mongolia Wesure Date Technology Co., Ltd. Hohhot, 010010, China; Inner Mongolia International Mongolian Hospital, Hohhot 010065, China
| | - Lei Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
| |
Collapse
|
15
|
Zhuang C, Liu Y, Gu R, Du S, Long Y. Prognostic signature of colorectal cancer based on uric acid-related genes. Heliyon 2023; 9:e22587. [PMID: 38213580 PMCID: PMC10782177 DOI: 10.1016/j.heliyon.2023.e22587] [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: 05/23/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 01/13/2024] Open
Abstract
Colorectal cancer (CRC) is one of the deadliest cancers worldwide. Numerous studies have reported a correlation between uric acid (UA) level and CRC risk. Here, we investigated the role and prognostic value of UA-related genes in CRC progression. CRC-associated gene expression and clinical data were retrieved from The Cancer Genome Atlas (TCGA), and UA-related genes were identified by overlapping the TCGA and GeneCards databases. The Gene Ontology annotation, Kyoto Encyclopedia of Genes and Genomes pathway, and Molecular Signatures Database dataset were subjected to gene set enrichment analysis. A prognostic model was constructed using the univariate and multivariate COX regression and least absolute shrinkage and selection operator (LASSO) analyses and validated using the Gene Expression Omnibus cohort. Competing endogenous RNA network, CellMiner, and Human Protein Atlas were used to detect the signature of 13 UA-related genes in the prediction model. The expression of five potential UA-related genes in CRC cell lines was confirmed via qPCR. CIBERSORT was used to evaluate immune cell infiltration in the TCGA-CRC dataset. Thirteen highly prognostic UA-related genes were used to construct a prognostic model of CRC with risk score accuracy and predictive efficacy. Abundance of activated M0 macrophages, monocytes, CD8+ T cells, and natural killer cells positively correlated with the risk score. Five promising UA-related genes showed higher expression levels in CRC than in colonic cell lines. Thus, our model posits a direct relationship between UA-related genes and CRC risk, offering novel insights into diagnosis, prognosis, and treatment.
Collapse
Affiliation(s)
- Chun Zhuang
- Department of Gastrointestinal Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yifan Liu
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ranran Gu
- Department of Clinical Laboratory, Yangpu Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Shanqing Du
- Department of Clinical Laboratory, Yangpu Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yin Long
- Department of Clinical Laboratory, Yangpu Hospital, School of Medicine, Tongji University, Shanghai, China
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| |
Collapse
|
16
|
Ho H, Yu SL, Chen HY, Yuan SS, Su KY, Hsu YC, Hsu CP, Chuang CY, Chang YH, Li YC, Cheng CL, Chang GC, Yang PC, Li KC. Whole exome sequencing and MicroRNA profiling of lung adenocarcinoma identified risk prediction features for tumors at stage I and its substages. Lung Cancer 2023; 184:107352. [PMID: 37657238 DOI: 10.1016/j.lungcan.2023.107352] [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: 05/02/2023] [Revised: 08/15/2023] [Accepted: 08/18/2023] [Indexed: 09/03/2023]
Abstract
OBJECTIVES About 20% of stage I lung adenocarcinoma (LUAD) patients suffer a relapse after surgical resection. While finer substages have been defined and refined in the AJCC staging system, clinical investigations on the tumor molecular landscape are lacking. MATERIALS AND METHODS We performed whole exome sequencing, DNA copy number and microRNA profiling on paired tumor-normal samples from a cohort of 113 treatment-naïve stage I Taiwanese LUAD patients. We searched for molecular features associated with relapse-free survival (RFS) of stage I or its substages and validated the findings with an independent Caucasian LUAD cohort. RESULTS We found sixteen nonsynonymous mutations harbored at EGFR, KRAS, TP53, CTNNB1 and six other genes associated with poor RFS in a dose-dependent manner via variant allele fraction (VAF). An index, maxVAF, was constructed to quantify the overall mutation load from genes other than EGFR. High maxVAF scores discriminated a small group of high-risk LUAD at stage I (median RFS: 4.5 versus 69.5 months; HR = 10.5, 95% CI = 4.22-26.12, P < 0.001). At the substage level, higher risk was found for patients with high maxVAF or high miR-31; IA (median RFS: 32.1 versus 122.8 months, P = 0.005) and IB (median RFS: 7.1 versus 26.2, P = 0.049). MicroRNAs, miR-182, miR-183 and miR-196a were found correlated with EGFR mutation and poor RFS in stage IB patients. CONCLUSION Distinctive features of somatic gene mutation and microRNA expression of stage I LUAD are characterized to complement the survival prognosis by substaging. The findings open up more options for precision management of stage I LUAD patients.
Collapse
Affiliation(s)
- Hao Ho
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Sung-Liang Yu
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan; Centers of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan; Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan; Institute of Medical Device and Imaging, College of Medicine, National Taiwan University, Taipei, Taiwan; Graduate Institute of Pathology, College of Medicine, National Taiwan University, Taipei, Taiwan; Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Hsuan-Yu Chen
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Shin-Sheng Yuan
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Kang-Yi Su
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan; Centers of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan; Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Yi-Chiung Hsu
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan, Taiwan
| | - Chung-Ping Hsu
- Division of Thoracic Surgery, Department of Surgery, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Cheng-Yen Chuang
- Division of Thoracic Surgery, Department of Surgery, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Ya-Hsuan Chang
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Yu-Cheng Li
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Chiou-Ling Cheng
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Gee-Chen Chang
- Division of Pulmonary Medicine, Department of Internal Medicine, Chung Shan Medical University Hospital, Taichung, Taiwan; Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan; School of Medicine, Chung Shan Medical University, Taichung, Taiwan; Division of Chest Medicine, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan; Institute of Biomedical Sciences, National Chung Hsing University, Taichung, Taiwan.
| | - Pan-Chyr Yang
- Centers of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan; Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan; Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.
| | - Ker-Chau Li
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan; Department of Statistics, University of California Los Angeles, Los Angeles, CA.
| |
Collapse
|
17
|
Pu T, Peddle A, Zhu J, Tejpar S, Verbandt S. Neoantigen identification: Technological advances and challenges. Methods Cell Biol 2023; 183:265-302. [PMID: 38548414 DOI: 10.1016/bs.mcb.2023.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
Neoantigens have emerged as promising targets for cutting-edge immunotherapies, such as cancer vaccines and adoptive cell therapy. These neoantigens are unique to tumors and arise exclusively from somatic mutations or non-genomic aberrations in tumor proteins. They encompass a wide range of alterations, including genomic mutations, post-transcriptomic variants, and viral oncoproteins. With the advancements in technology, the identification of immunogenic neoantigens has seen rapid progress, raising new opportunities for enhancing their clinical significance. Prediction of neoantigens necessitates the acquisition of high-quality samples and sequencing data, followed by mutation calling. Subsequently, the pipeline involves integrating various tools that can predict the expression, processing, binding, and recognition potential of neoantigens. However, the continuous improvement of computational tools is constrained by the availability of datasets which contain validated immunogenic neoantigens. This review article aims to provide a comprehensive summary of the current knowledge as well as limitations in neoantigen prediction and validation. Additionally, it delves into the origin and biological role of neoantigens, offering a deeper understanding of their significance in the field of cancer immunotherapy. This article thus seeks to contribute to the ongoing efforts to harness neoantigens as powerful weapons in the fight against cancer.
Collapse
Affiliation(s)
- Ting Pu
- Digestive Oncology Unit, KULeuven, Leuven, Belgium
| | | | - Jingjing Zhu
- de Duve Institute, Université catholique de Louvain, Brussels, Belgium
| | | | | |
Collapse
|
18
|
Aledo-Serrano Á, Valls-Carbó A, Fenger CD, Groeppel G, Hartlieb T, Pascual I, Herraez E, Cabal B, García-Morales I, Toledano R, Budke M, Beltran-Corbellini Á, Baldassari S, Coras R, Kobow K, Herrera DM, Del Barrio A, Dahl HA, Del Pino I, Baulac S, Blumcke I, Møller RS, Gil-Nagel A. D-galactose Supplementation for the Treatment of Mild Malformation of Cortical Development with Oligodendroglial Hyperplasia in Epilepsy (MOGHE): A Pilot Trial of Precision Medicine After Epilepsy Surgery. Neurotherapeutics 2023; 20:1294-1304. [PMID: 37278968 PMCID: PMC10480113 DOI: 10.1007/s13311-023-01395-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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/22/2023] [Indexed: 06/07/2023] Open
Abstract
MOGHE is defined as mild malformation of cortical development with oligodendroglial hyperplasia in epilepsy. Approximately half of the patients with histopathologically confirmed MOGHE carry a brain somatic variant in the SLC35A2 gene encoding a UDP-galactose transporter. Previous research showed that D-galactose supplementation results in clinical improvement in patients with a congenital disorder of glycosylation due to germline variants in SLC35A2. We aimed to evaluate the effects of D-galactose supplementation in patients with histopathologically confirmed MOGHE, with uncontrolled seizures or cognitive impairment and epileptiform activity at the EEG after epilepsy surgery (NCT04833322). Patients were orally supplemented with D-galactose for 6 months in doses up to 1.5 g/kg/day and monitored for seizure frequency including 24-h video-EEG recording, cognition and behavioral scores, i.e., WISC, BRIEF-2, SNAP-IV, and SCQ, and quality of life measures, before and 6 months after treatment. Global response was defined by > 50% improvement of seizure frequency and/or cognition and behavior (clinical global impression of "much improved" or better). Twelve patients (aged 5-28 years) were included from three different centers. Neurosurgical tissue samples were available in all patients and revealed a brain somatic variant in SLC35A2 in six patients (non-present in the blood). After 6 months of supplementation, D-galactose was well tolerated with just two patients presenting abdominal discomfort, solved after dose spacing or reduction. There was a 50% reduction or higher of seizure frequency in 3/6 patients, with an improvement at EEG in 2/5 patients. One patient became seizure-free. An improvement of cognitive/behavioral features encompassing impulsivity (mean SNAP-IV - 3.19 [- 0.84; - 5.6]), social communication (mean SCQ - 2.08 [- 0.63; - 4.90]), and executive function (BRIEF-2 inhibit - 5.2 [- 1.23; - 9.2]) was observed. Global responder rate was 9/12 (6/6 in SLC35A2-positive). Our results suggest that supplementation with D-galactose in patients with MOGHE is safe and well tolerated and, although the efficacy data warrant larger studies, it might build a rationale for precision medicine after epilepsy surgery.
Collapse
Affiliation(s)
- Ángel Aledo-Serrano
- Epilepsy and Neurogenetics Program, Ruber Internacional Hospital, La Masó 34, 28034, Madrid, Spain.
- Initiative for Neuroscience (INCE) Foundation, Madrid, Spain.
- Neuroscience Institute, Vithas Madrid La Milagrosa University Hospital, Vithas Hospital Group, Madrid, Spain.
| | - Adrián Valls-Carbó
- Epilepsy and Neurogenetics Program, Ruber Internacional Hospital, La Masó 34, 28034, Madrid, Spain
- Initiative for Neuroscience (INCE) Foundation, Madrid, Spain
| | - Christina D Fenger
- Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Centre, Dianalund, Denmark
- Amplexa Genetics A/S (H.A.D.), Odense, Denmark
| | - Gudrun Groeppel
- Department of Paediatrics and Adolescent Medicine and Department of Neurology, Johannes Kepler University Linz, Kepler University Hospital, Linz, Austria
| | - Till Hartlieb
- Center for Pediatric Neurology, Neurorehabilitation, and Epileptology, Schoen Clinic, Vogtareuth, Germany
- Research Institute "Rehabilitation, " PMU Salzburg, Transition, PalliationSalzburg, Austria
| | - Irene Pascual
- Epilepsy and Neurogenetics Program, Ruber Internacional Hospital, La Masó 34, 28034, Madrid, Spain
| | - Erika Herraez
- Epilepsy and Neurogenetics Program, Ruber Internacional Hospital, La Masó 34, 28034, Madrid, Spain
- Department of Neurophysiology, Rey Juan Carlos University Hospital, Madrid, Spain
| | - Borja Cabal
- Epilepsy and Neurogenetics Program, Ruber Internacional Hospital, La Masó 34, 28034, Madrid, Spain
- Department of Neurology, Puerta de Hierro University Hospital, Madrid, Spain
| | - Irene García-Morales
- Epilepsy and Neurogenetics Program, Ruber Internacional Hospital, La Masó 34, 28034, Madrid, Spain
- Epilepsy Unit, Department of Neurology, Clinico San Carlos University Hospital, Madrid, Spain
| | - Rafael Toledano
- Epilepsy and Neurogenetics Program, Ruber Internacional Hospital, La Masó 34, 28034, Madrid, Spain
- Epilepsy Unit, Department of Neurology, Clinico San Carlos University Hospital, Madrid, Spain
| | - Marcelo Budke
- Epilepsy and Neurogenetics Program, Ruber Internacional Hospital, La Masó 34, 28034, Madrid, Spain
- Department of Neurosurgery, Niño Jesus University Hospital, Madrid, Spain
| | | | - Sara Baldassari
- Sorbonne Université, Institut du Cerveau-Paris Brain Institute-ICM, Inserm, CNRS, Paris, France
| | - Roland Coras
- Department of Neuropathology, University Hospital, Erlangen, Germany
| | - Katja Kobow
- Department of Neuropathology, University Hospital, Erlangen, Germany
| | - David M Herrera
- Epilepsy and Neurogenetics Program, Ruber Internacional Hospital, La Masó 34, 28034, Madrid, Spain
- Epilepsy Unit, Department of Neurology, Kennedy University Hospital, Bogota, Colombia
| | - Antonio Del Barrio
- Epilepsy and Neurogenetics Program, Ruber Internacional Hospital, La Masó 34, 28034, Madrid, Spain
| | | | - Isabel Del Pino
- Institute of Neurosciences (IN), Higher Council for Scientific Research-Miguel Hernandez University, Alicante, Spain
| | - Stéphanie Baulac
- Sorbonne Université, Institut du Cerveau-Paris Brain Institute-ICM, Inserm, CNRS, Paris, France
| | - Ingmar Blumcke
- Department of Neuropathology, University Hospital, Erlangen, Germany
| | - Rikke S Møller
- Neuroscience Institute, Vithas Madrid La Milagrosa University Hospital, Vithas Hospital Group, Madrid, Spain
- Department of Regional Health Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Antonio Gil-Nagel
- Epilepsy and Neurogenetics Program, Ruber Internacional Hospital, La Masó 34, 28034, Madrid, Spain
- Initiative for Neuroscience (INCE) Foundation, Madrid, Spain
| |
Collapse
|
19
|
Zhang B, He R, Xu Z, Sun Y, Wei L, Li L, Liu Y, Guo W, Song L, Wang H, Lin Z, Ma L. Somatic mutation spectrum of a Chinese cohort of pediatrics with vascular malformations. Orphanet J Rare Dis 2023; 18:261. [PMID: 37658401 PMCID: PMC10474751 DOI: 10.1186/s13023-023-02860-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 08/20/2023] [Indexed: 09/03/2023] Open
Abstract
BACKGROUND Somatic mutations of cancer driver genes are found to be responsible for vascular malformations with clinical manifestations ranging from cutaneous birthmarks to life-threatening systemic anomalies. Till now, only a limited number of cases and mutations were reported in Chinese population. The purpose of this study was to describe the somatic mutation spectrum of a cohort of Chinese pediatrics with vascular malformations. METHODS Pediatrics diagnosed with various vascular malformations were collected between May 2019 and October 2020 from Beijing Children's Hospital. Genomic DNA of skin lesion of each patient was extracted and sequenced by whole-exome sequencing to identify pathogenic somatic mutations. Mutations with variant allele frequency less than 5% were validated by ultra-deep sequencing. RESULTS A total of 67 pediatrics (33 males, 34 females, age range: 0.1-14.8 years) were analyzed. Exome sequencing identified somatic mutations of corresponding genes in 53 patients, yielding a molecular diagnosis rate of 79.1%. Among 29 PIK3CA mutations, 17 were well-known hotspot p.E542K, p.E545K and p.H1047R/L. Non-hotspot mutations were prevalent in patients with PIK3CA-related overgrowth spectrum, accounting for 50.0% (11/22) of detected mutations. The hotspot GNAQ p.R183Q and TEK p.L914F mutations were responsible for the majority of port-wine stain/Sturge-Weber syndrome and venous malformation, respectively. In addition, we identified a novel AKT1 p.Q79K mutation in Proteus syndrome and MAP3K3 p.E387D mutation in verrucous venous malformation. CONCLUSIONS The somatic mutation spectrum of vascular malformations in Chinese population is similar to that reported in other populations, but non-hotspot PIK3CA mutations may also be prevalent. Molecular diagnosis may help the clinical diagnosis, treatment and management of these pediatric patients with vascular malformations.
Collapse
Affiliation(s)
- Bin Zhang
- Department of Dermatology, Beijing Children's Hospital, Capital Medical University (National Center for Children's Health, China), No. 56 Nanlishi Road, Xicheng District, Beijing, 100045, China.
- Department of Dermatology, Zhengzhou University, Affiliated Children's Hospital, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450000, Henan, China.
| | - Rui He
- Department of Dermatology, Beijing Children's Hospital, Capital Medical University (National Center for Children's Health, China), No. 56 Nanlishi Road, Xicheng District, Beijing, 100045, China
| | - Zigang Xu
- Department of Dermatology, Beijing Children's Hospital, Capital Medical University (National Center for Children's Health, China), No. 56 Nanlishi Road, Xicheng District, Beijing, 100045, China
| | - Yujuan Sun
- Department of Dermatology, Beijing Children's Hospital, Capital Medical University (National Center for Children's Health, China), No. 56 Nanlishi Road, Xicheng District, Beijing, 100045, China
| | - Li Wei
- Department of Dermatology, Beijing Children's Hospital, Capital Medical University (National Center for Children's Health, China), No. 56 Nanlishi Road, Xicheng District, Beijing, 100045, China
| | - Li Li
- Department of Dermatology, Beijing Children's Hospital, Capital Medical University (National Center for Children's Health, China), No. 56 Nanlishi Road, Xicheng District, Beijing, 100045, China
| | - Yuanxiang Liu
- Department of Dermatology, Beijing Children's Hospital, Capital Medical University (National Center for Children's Health, China), No. 56 Nanlishi Road, Xicheng District, Beijing, 100045, China
| | - Wu Guo
- Department of Dermatology, Zhengzhou University, Affiliated Children's Hospital, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450000, Henan, China
| | - Li Song
- Department of Dermatology, Zhengzhou University, Affiliated Children's Hospital, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450000, Henan, China
| | - Huijun Wang
- Dermatology Hospital, Southern Medical University, No.2 Lujing Road, Guangzhou, 510091, China
| | - Zhimiao Lin
- Dermatology Hospital, Southern Medical University, No.2 Lujing Road, Guangzhou, 510091, China.
| | - Lin Ma
- Department of Dermatology, Beijing Children's Hospital, Capital Medical University (National Center for Children's Health, China), No. 56 Nanlishi Road, Xicheng District, Beijing, 100045, China.
| |
Collapse
|
20
|
Shuaib M, Singh AK, Gupta S, Alasmari AF, Alqahtani F, Kumar S. Designing of neoepitopes based vaccine against breast cancer using integrated immuno and bioinformatics approach. J Biomol Struct Dyn 2023:1-14. [PMID: 37584493 DOI: 10.1080/07391102.2023.2247081] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2023]
Abstract
Cancer is characterized by genetic instability due to accumulation of somatic mutations in the genes which generate neoepitopes (mutated epitopes) for targeting by Cytotoxic T lymphocytes (CTL). Breast cancer has a high transformation rate with unique composition of mutational burden and neoepitopes load that open a platform to designing a neoepitopes-based vaccine. Neoepitopes-based therapeutic cancer vaccines designed by neoantigens have shown to be feasible, nontoxic, and immunogenic in cancer patients. Stimulation of CTL by neoepitope-based vaccine of self-antigenic proteins plays a key role in distinguishing cancer cells from normal cells and selectively targets only malignant cells. A neoepitopes-based vaccine to combat breast cancer was designed by combining immunology and bioinformatics approaches. The vaccine construct was assembled by the fusion of CTL neoepitopes, helper sequences (used for better separation of the epitopes), and adjuvant together with linkers. The neoepitopes were identified from somatic mutations in the MUC16, TP53, RYR2, F5, DNAH17, ASPM, and ABCA13 self-antigenic proteins. The vaccine construct was undertaken to study the immune simulations (IS), physiochemical characteristics (PP), molecular docking (MD) and simulations, and cloning in appropriate vector. Together, these parameters establish safety, stability, and a strong binding affinity against class I MHC molecules capable of inducing a complete immune response against breast cancer cells.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Mohd Shuaib
- Department of Biochemistry, Molecular Signaling & Drug Discovery Laboratory, Central University of Punjab, Bathinda, India
| | - Atul Kumar Singh
- Department of Biochemistry, Molecular Signaling & Drug Discovery Laboratory, Central University of Punjab, Bathinda, India
| | - Sanjay Gupta
- Department of Urology, Case Western Reserve University, Cleveland, OH, USA
| | - Abdullah F Alasmari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Flaeh Alqahtani
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Shashank Kumar
- Department of Biochemistry, Molecular Signaling & Drug Discovery Laboratory, Central University of Punjab, Bathinda, India
| |
Collapse
|
21
|
Sun Y, Li Z, Sun J, Ma D, Shan X, Chen X. Somatic Mutation of PRKAR1A in Four Cases of Sporadic Cardiac Myxoma. Arch Iran Med 2023; 26:346-354. [PMID: 38310436 PMCID: PMC10685830 DOI: 10.34172/aim.2023.52] [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] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 03/02/2022] [Indexed: 02/05/2024]
Abstract
BACKGROUND Inactivating mutations of the protein kinase A regulatory subunit 1 alpha (PRKAR1A) gene have been reported in familial cardiac myxoma. However, the role of PRKAR1A mutation in sporadic cardiac myxoma remains unknown. METHODS Targeted next-generation sequencing (NGS) was performed to identify mutations with the PRKAR1A gene in seven cases of sporadic cardiac myxomas. Sanger sequencing of DNA from cardiac myxoma specimens and matched peripheral blood samples was performed to verify the identified mutations. RESULTS Targeted NGS of myxoma DNA revealed 232 single nucleotide variants in 141 genes and 38 insertion-deletion mutations in 13 genes. Six PRKAR1A mutations were identified in four of the seven cardiac myxoma cases, and thus, the PRKAR1A inactivating mutation rate was 57.2% (4/7, 95% CI=0.44-0.58, P<0.05). The PRKAR1A variants identified by Sanger sequencing analysis were consistent with those from the NGS analysis for the four myxoma specimens. All of the pathogenic PRKAR1A mutations led to premature termination of PRKAR1A, except for one synonymous mutation. Moreover, none of the nonsense and missense mutations found in the myxoma specimens were found in the matched peripheral blood samples. CONCLUSION Pathogenic mutations of the PRKAR1A gene were identified in tumor specimens from four cases of sporadic cardiac myxoma, and the absence of these mutations in peripheral blood samples demonstrated that they were somatic mutations.
Collapse
Affiliation(s)
- Yunpeng Sun
- Department of Cardiac Surgery, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Zhiping Li
- Department of Pharmacology, Basic Medical College of Jilin University, Changchun, Jilin, 130021, China
| | - Jingnan Sun
- Department of Hematology, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Dashi Ma
- Department of Cardiac Surgery, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Xue Shan
- Department of Cardiac Surgery, The First Hospital of Jilin University, Changchun, Jilin, 130021, China
| | - Xia Chen
- Department of Pharmacology, Basic Medical College of Jilin University, Changchun, Jilin, 130021, China
| |
Collapse
|
22
|
Wu J, Chen W, Zhou Y, Chi Y, Hua X, Wu J, Gu X, Chen S, Zhou Z. TSNAdb v2.0: The Updated Version of Tumor-specific Neoantigen Database. Genomics Proteomics Bioinformatics 2023; 21:259-266. [PMID: 36209954 PMCID: PMC10626054 DOI: 10.1016/j.gpb.2022.09.012] [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] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 09/24/2022] [Accepted: 09/30/2022] [Indexed: 11/05/2022]
Abstract
In recent years, neoantigens have been recognized as ideal targets for tumor immunotherapy. With the development of neoantigen-based tumor immunotherapy, comprehensive neoantigen databases are urgently needed to meet the growing demand for clinical studies. We have built the tumor-specific neoantigen database (TSNAdb) previously, which has attracted much attention. In this study, we provide TSNAdb v2.0, an updated version of the TSNAdb. TSNAdb v2.0 offers several new features, including (1) adopting more stringent criteria for neoantigen identification, (2) providing predicted neoantigens derived from three types of somatic mutations, and (3) collecting experimentally validated neoantigens and dividing them according to the experimental level. TSNAdb v2.0 is freely available at https://pgx.zju.edu.cn/tsnadb/.
Collapse
Affiliation(s)
- Jingcheng Wu
- Institute of Drug Metabolism and Pharmaceutical Analysis and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wenfan Chen
- Institute of Drug Metabolism and Pharmaceutical Analysis and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuxuan Zhou
- Institute of Drug Metabolism and Pharmaceutical Analysis and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ying Chi
- Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Alibaba DAMO Academy, Hangzhou 311121, China
| | - Xiansheng Hua
- Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Alibaba DAMO Academy, Hangzhou 311121, China
| | - Jian Wu
- The Second Affiliated Hospital of School of Medicine, and School of Public Health, Zhejiang University, Hangzhou 310058, China; Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou 310018, China
| | - Xun Gu
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Shuqing Chen
- Institute of Drug Metabolism and Pharmaceutical Analysis and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhan Zhou
- Institute of Drug Metabolism and Pharmaceutical Analysis and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Alibaba DAMO Academy, Hangzhou 311121, China; Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou 310018, China.
| |
Collapse
|
23
|
Bhushan S, Singh AK, Thakur Y, Baskar R. Persistence of parental age effect on somatic mutation rates across generations in Arabidopsis. BMC Plant Biol 2023; 23:152. [PMID: 36944916 PMCID: PMC10031922 DOI: 10.1186/s12870-023-04150-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
In the model plant Arabidopsis thaliana, parental age is known to affect somatic mutation rates in their immediate progeny and here we show that this age dependent effect persists across successive generations. Using a set of detector lines carrying the mutated uidA gene, we examined if a particular parental age maintained across five consecutive generations affected the rates of base substitution (BSR), intrachromosomal recombination (ICR), frameshift mutation (FS), and transposition. The frequency of functional GUS reversions were assessed in seedlings as a function of identical/different parental ages across generations. In the context of a fixed parental age, BSR/ICR rates were unaffected in the first three generations, then dropped significantly in the 4th and increased in most instances in the 5th generation (e.g. BSR (F1 38 = 0.9, F2 38 = 1.14, F3 38 = 1.02, F4 38 = 0.5, F5 38 = 0.76)). On the other hand, with advancing parental ages, BSR/ICR rates remained high in the first two/three generations, with a striking resemblance in the pattern of mutation rates (BSR (F1 38 = 0.9, F1 43 = 0.53, F1 48 = 0.79, F1 53 = 0.83 and F2 38 = 1.14, F2 43 = 0.57, F2 48 = 0.64, F2 53 = 0.94). We adopted a novel approach of identifying and tagging flowers pollinated on a particular day, thereby avoiding biases due to potential emasculation induced stress responses. Our results suggest a time component in counting the number of generations a plant has passed through self-fertilization at a particular age in determining the somatic mutation rates.
Collapse
Affiliation(s)
- Shashi Bhushan
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology-Madras, Chennai, 600 036, India
| | - Amit Kumar Singh
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
- Institut de Biologie Moléculaire des Plantes, UPR2357 CNRS, Université de Strasbourg, 12 rue du Général Zimmer, Strasbourg Cédex, 67084, France
| | - Yogendra Thakur
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology-Madras, Chennai, 600 036, India
| | - Ramamurthy Baskar
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology-Madras, Chennai, 600 036, India.
| |
Collapse
|
24
|
Gerald T, Margulis V, Meng X, Bagrodia A, Cole S, Qin Q, Call SG, Mauer E, Lotan Y, Woldu SL. Actionable genomic landscapes from a real-world cohort of urothelial carcinoma patients. Urol Oncol 2023; 41:148.e17-148.e24. [PMID: 36653279 DOI: 10.1016/j.urolonc.2022.12.008] [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: 10/12/2022] [Revised: 12/17/2022] [Accepted: 12/23/2022] [Indexed: 01/18/2023]
Abstract
BACKGROUND Recent targeted therapies for advanced and metastatic urothelial cancer have generated enthusiasm, but the actionable genomic landscape of early-stage disease remains largely unknown. Here, we utilized a large, real-world cohort to comprehensively investigate the incidence of genetic alterations with potential therapeutic implications at all stages of bladder cancer. MATERIALS AND METHODS We retrospectively analyzed next-generation sequencing (NGS) data from 1,562 bladder cancer patients (stages I-IV) with formalin-fixed, paraffin-embedded tumor biopsies sequenced using the Tempus xT solid tumor assay. Incidence of genetic alterations, tumor mutational burden (TMB), microsatellite instability (MSI), and PD-L1 status were assessed and stratified by bladder cancer stage. For patients with tumor-normal match sequencing (n=966), incidental germline alterations in 50 genes were assessed. RESULTS The cohort was composed of 165 stage I-II, 211 stage III, and 1,186 stage IV tumors. TMB-high, PD-L1 positive, and MSI-high status were noted in 14%, 33%, and 0.7% of tumors, respectively, and were similar across stages. Alterations in fibroblast growth factor receptor (FGFR)2/3, homologous recombination repair genes, additional DNA repair gene mutations (ERCC2, RB1, FANCC), and NTRK fusions were detected at similar frequencies across disease stages. We identified a low rate of incidental germline mutations in all tumors (5.2%) and in specific genes: MUTYH (1.9%), BRCA2 (0.5%), and ATM (0.8%). CONCLUSIONS Important subsets of patients demonstrate genetic alterations in potentially actionable molecular pathways at all stages. This analysis found minimal variability in these alterations across stages, providing rationale for early identification of genetic alterations and personalization of therapies at all stages for patients with bladder cancer.
Collapse
Affiliation(s)
- Thomas Gerald
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX.
| | - Vitaly Margulis
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Xiaosong Meng
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Aditya Bagrodia
- Department of Urology, University of California San Diego, San Diego, CA
| | - Suzanne Cole
- Division of Hematology Oncology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX
| | - Qian Qin
- Division of Hematology Oncology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX
| | | | | | - Yair Lotan
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Solomon L Woldu
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX
| |
Collapse
|
25
|
Liao G, Tang J, Bai J. Early development of esophageal squamous cell cancer: Stem cells, cellular origins and early clone evolution. Cancer Lett 2023; 555:216047. [PMID: 36587837 DOI: 10.1016/j.canlet.2022.216047] [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: 11/04/2022] [Revised: 12/08/2022] [Accepted: 12/24/2022] [Indexed: 12/31/2022]
Abstract
Esophageal squamous cell carcinoma (ESCC), a highly malignant cancer with poor prognosis, is an example of the classical view of cancer development based on stem cell origin and multistep progression. In the past five years, the applications of large-scale sequencing and single-cell sequencing have expanded to human esophageal normal tissues and precancerous lesions, which, coupled with the application of transgenic lineage tracing technology in mouse models, has provided a more comprehensive and detailed understanding of esophageal stem cell heterogeneity and early clonal evolution of ESCC. In this review, we discuss the heterogeneity of esophageal basal-layer stem cells and their potential relationship with cells of ESCC origin. We present evidence that expansion of NOTCH1 mutants may call into play an evolutionarily conserved anti-cancer mechanism and mold the model of early clonal evolution in ESCCs. Finally, we discuss the potential avenues in this context. This review provides a focused understanding of the early development of ESCC, as a background for early tumor detection, intervention, and prevention strategies.
Collapse
Affiliation(s)
- Guobin Liao
- Department of Gastroenterology, Second Affiliated Hospital, Army Medical University, Chongqing, 400037, China; Department of Gastroenterology, The 901 Hospital of Chinese People's Liberation Army Joint Service Support Unit, Hefei, 230000, China.
| | - Jun Tang
- Department of Gastroenterology, The 901 Hospital of Chinese People's Liberation Army Joint Service Support Unit, Hefei, 230000, China.
| | - Jianying Bai
- Department of Gastroenterology, Second Affiliated Hospital, Army Medical University, Chongqing, 400037, China.
| |
Collapse
|
26
|
Quan C, Liu F, Qi L, Tie Y. LRT-CLUSTER: A New Clustering Algorithm Based on Likelihood Ratio Test to Identify Driving Genes. Interdiscip Sci 2023; 15:217-230. [PMID: 36848004 DOI: 10.1007/s12539-023-00554-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 03/01/2023]
Abstract
Somatic mutations often occur at high relapse sites in protein sequences, which indicates that the location clustering of somatic missense mutations can be used to identify driving genes. However, the traditional clustering algorithm has such problems as the background signal over-fitting, the clustering algorithm is not suitable for mutation data, and the performance of identifying low-frequency mutation genes needs to be improved. In this paper, we propose a linear clustering algorithm based on likelihood ratio test knowledge to identify driver genes. In this experiment, firstly, the polynucleotide mutation rate is calculated based on the prior knowledge of likelihood ratio test. Then, the simulation data set is obtained through the background mutation rate model. Finally, the unsupervised peak clustering algorithm is used to, respectively, evaluate the somatic mutation data and the simulation data to identify the driver genes. The experimental results show that our method achieves a better balance of precision and sensitivity. It can also identify the driver genes missed by other methods, making it an effective supplement to other methods. We also discover some potential linkages between genes and between genes and mutation sites, which is of great value to target drug therapy research. Method framework: Our proposed model framework is as follows. a. Counting mutation sites and the number of mutations in tumor gene elements. b. The nucleotide context mutation frequency is counted based on the likelihood ratio test knowledge, and the background mutation rate model is obtained. c. Based on Monte Carlo simulation method, data sets with the same number of mutations as gene elements are randomly sampled to obtain simulated mutation data, and the sampling frequency of each mutation site is related to the mutation rate of polynucleotide. d. The original mutation data and the simulated mutation data after random reconstruction are clustered by peak density, respectively, and the corresponding clustering scores are obtained. e. We can obtain the clustering information statistics in each gene segment and score of each gene segment from the original single nucleotide mutation data through step d. f. According to the observed score and the simulated clustering score, the p-value of the corresponding gene fragment is calculated. g. We can obtain the clustering information statistics in each gene segment and score of each gene segment from the simulated single nucleotide mutation data through step d.
Collapse
Affiliation(s)
- Chenxu Quan
- School of Electrical and Information Engineering, Zhengzhou University, Zhengzhou, China.,Department of Respiratory and Sleep Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Fenghui Liu
- Department of Respiratory and Sleep Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Lin Qi
- School of Electrical and Information Engineering, Zhengzhou University, Zhengzhou, China
| | - Yun Tie
- School of Electrical and Information Engineering, Zhengzhou University, Zhengzhou, China.
| |
Collapse
|
27
|
Ludwig LS, Lareau CA. Concomitant Sequencing of Accessible Chromatin and Mitochondrial Genomes in Single Cells Using mtscATAC-Seq. Methods Mol Biol 2023; 2611:269-282. [PMID: 36807073 DOI: 10.1007/978-1-0716-2899-7_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Mitochondria are unique organelles of eukaryotic cells that carry their own multicopy number and circular genome. In most mammals, including humans and mice, the size of the chromosome is ~16,000 base pairs and unlike nuclear DNA, mitochondrial DNA (mtDNA) is not densely compacted. This results in mtDNA to be highly accessible for enzymes such as the Tn5 transposase, commonly used for accessible chromatin profiling of nuclear chromatinized DNA. Here, we describe a method for the concomitant sequencing of mtDNA and accessible chromatin in thousands of individual cells via the mitochondrial single-cell assay for transposase accessible chromatin by sequencing (mtscATAC-seq). Our approach extends the utility of existing scATAC-seq products and protocols as we (Nam et al, Nat Rev Genet 22:3-18, 2021) fix cells using formaldehyde to retain mitochondria and its mtDNA within its originating cell, (Buenrostro et al, Nat Methods 10:1213-1218, 2013) modify lysis conditions to permeabilize cells and mitochondria, and (Corces et al, Nat Methods 14:959-962, 2017) optimize bioinformatic processing protocols to collectively increase mitochondrial genome coverage for downstream analysis. Here, we discuss the essentials for the experimental and computational methodologies to generate and analyze thousands of multiomic profiles of single cells over the course of a few days, enabling the profiling of accessible chromatin and mtDNA genotypes to reconstruct clonal relationships and studies of mitochondrial genetics and disease.
Collapse
Affiliation(s)
- Leif S Ludwig
- Berlin Institute of Health at Charité Universitätsmedizin Berlin, Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Caleb A Lareau
- Departments of Genetics and Pathology, Stanford University, Stanford, CA, USA.
| |
Collapse
|
28
|
Yun J, Song H, Kim SM, Kim S, Kwon SR, Lee YE, Jeong D, Park JH, Kwon S, Yun H, Lee DS. Analysis of clinical and genomic profiles of therapy-related myeloid neoplasm in Korea. Hum Genomics 2023; 17:13. [PMID: 36814285 PMCID: PMC9948421 DOI: 10.1186/s40246-023-00458-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 02/07/2023] [Indexed: 02/24/2023] Open
Abstract
BACKGROUND Therapy-related myeloid neoplasm (T-MN) rarely occurs among cancer survivors, and was characterized by poor prognosis. T-MN has germline predisposition in a considerable proportion. Here, clinical characteristics and germline/somatic variant profiles in T-MN patients were investigated, and the findings were compared with those of previous studies. METHODS A review of medical records, cytogenetic study, targeted sequencing by next-generation sequencing, and survival analysis were performed on 53 patients with T-MN at a single institution in Korea. RESULTS The patients were relatively younger compared to T-MN patients in other studies. Our T-MN patients showed a high frequency of complex karyotypes, -5/del(5q), and -7/del(7q), which was similar to the Japanese study group but higher than the Australian study group. The most common primary disease was non-Hodgkin lymphoma, followed by breast cancer. The detailed distributions of primary diseases were different across study groups. Seven patients (13.2%) harbored deleterious presumed/potential germline variants in cancer predisposition genes (CPG) such as BRIP1, CEBPA, DDX41, FANCM, NBN, NF1, and RUNX1. In the somatic variant profile, TP53 was the most frequently mutated gene, which was consistent with the previous studies about T-MN. However, the somatic variant frequency in our study group was lower than in other studies. Adverse factors for overall survival were male sex, older age, history of previous radiotherapy, previous longer cytotoxic therapy, and -5/del(5q). CONCLUSION The findings of our study corroborate important information about T-MN patients. As well as a considerable predisposition to CPG, the clinical characteristics and somatic variant profile showed distinctive patterns. Germline variant testing should be recommended for T-MN patients. If the T-MN patients harbor pathogenic germline variants, the family members for stem cell donation should be screened for carrier status through germline variant testing to avoid donor-derived myeloid neoplasm. For the prediction of the prognosis in T-MN patients, sex, age, past treatment history, and cytogenetic findings can be considered.
Collapse
Affiliation(s)
- Jiwon Yun
- Department of Laboratory Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
- Department of Laboratory Medicine, Chung-Ang University Hospital, Seoul, Republic of Korea
| | - Hyojin Song
- Department of Genomic Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Sung-Min Kim
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Soonok Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Seok Ryun Kwon
- Department of Laboratory Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Young Eun Lee
- Department of Laboratory Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Dajeong Jeong
- Department of Laboratory Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Jae Hyeon Park
- Department of Laboratory Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Sunghoon Kwon
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
- Bio-MAX Institute, Seoul National University, Seoul, Republic of Korea
| | - Hongseok Yun
- Department of Genomic Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.
| | - Dong Soon Lee
- Department of Laboratory Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.
- Genomic Medicine Institute, Seoul National University Medical Research Center, Seoul, Republic of Korea.
| |
Collapse
|
29
|
Blum N, Harris MP. Localized heterochrony integrates overgrowth potential of oncogenic clones. Dis Model Mech 2023; 16:286292. [PMID: 36621776 PMCID: PMC9932785 DOI: 10.1242/dmm.049793] [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: 07/28/2022] [Accepted: 12/23/2022] [Indexed: 01/10/2023] Open
Abstract
Somatic mutations occur frequently and can arise during embryogenesis, resulting in the formation of a patchwork of mutant clones. Such mosaicism has been implicated in a broad range of developmental anomalies; however, their etiology is poorly understood. Patients carrying a common somatic oncogenic mutation in either PIK3CA or AKT1 can present with disproportionally large digits or limbs. How mutant clones, carrying an oncogenic mutation that often drives unchecked proliferation, can lead to controlled and coordinated overgrowth is unknown. We use zebrafish to explore the growth dynamics of oncogenic clones during development. Here, in a subset of clones, we observed a local increase in proportion of the fin skeleton closely resembling overgrowth phenotypes in patients. We unravel the cellular and developmental mechanisms of these overgrowths, and pinpoint the cell type and timing of clonal expansion. Coordinated overgrowth is associated with rapid clone expansion during early pre-chondrogenic phase of bone development, inducing a heterochronic shift that drives the change in bone size. Our study details how development integrates and translates growth potential of oncogenic clones, thereby shaping the phenotypic consequences of somatic mutations.
Collapse
Affiliation(s)
- Nicola Blum
- Department of Orthopaedics, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, USA.,Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Matthew P Harris
- Department of Orthopaedics, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, USA.,Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| |
Collapse
|
30
|
Perez-Rodriguez D, Kalyva M, Santucci C, Proukakis C. Somatic CNV Detection by Single-Cell Whole-Genome Sequencing in Postmortem Human Brain. Methods Mol Biol 2023; 2561:205-230. [PMID: 36399272 DOI: 10.1007/978-1-0716-2655-9_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The evidence for a role of somatic mutations, including copy-number variants (CNVs), in neurodegeneration has increased in the last decade. However, the understanding of the types and origins of these mutations, and their exact contributions to disease onset and progression, is still in its infancy. The use of single-cell (or nuclear) whole-genome sequencing (scWGS) has emerged as a powerful tool to answer these questions. In the present chapter, we provide laboratory and bioinformatic protocols used successfully in our lab to detect megabase-scale CNVs in single cells from multiple system atrophy (MSA) human postmortem brains, using immunolabeling prior to selection of nuclei for whole-genome amplification (WGA). We also present an unpublished comparison of scWGS generated from the same control substantia nigra (SN) sample, using the latest versions of popular WGA chemistries, MDA and PicoPLEX. We have used this protocol to focus on brain cell types most relevant to synucleinopathies (dopaminergic [DA] neurons in Parkinson's disease [PD] and oligodendrocytes in MSA), but it can be applied to any tissue and/or cell type with appropriate markers.
Collapse
Affiliation(s)
- Diego Perez-Rodriguez
- Department of Clinical and Movement Neurosciences, Queen Square Institute of Neurology, University College London, London, UK
| | - Maria Kalyva
- Department of Clinical and Movement Neurosciences, Queen Square Institute of Neurology, University College London, London, UK
| | - Catherine Santucci
- Department of Clinical and Movement Neurosciences, Queen Square Institute of Neurology, University College London, London, UK
| | - Christos Proukakis
- Department of Clinical and Movement Neurosciences, Queen Square Institute of Neurology, University College London, London, UK.
| |
Collapse
|
31
|
López-Nevado M, Ortiz-Martín J, Serrano C, Pérez-Saez MA, López-Lorenzo JL, Gil-Etayo FJ, Rodríguez-Frías E, Cabrera-Marante O, Morales-Pérez P, Rodríguez-Pinilla MS, Manso R, Salgado-Sánchez RN, Cerdá-Montagud A, Quesada-Espinosa JF, Gómez-Rodríguez MJ, Paz-Artal E, Muñoz-Calleja C, Arranz-Sáez R, Allende LM. Novel Germline TET2 Mutations in Two Unrelated Patients with Autoimmune Lymphoproliferative Syndrome-Like Phenotype and Hematologic Malignancy. J Clin Immunol 2023; 43:165-180. [PMID: 36066697 DOI: 10.1007/s10875-022-01361-y] [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: 05/11/2022] [Accepted: 08/26/2022] [Indexed: 01/18/2023]
Abstract
Somatic mutations in the ten-eleven translocation methylcytosine dioxygenase 2 gene (TET2) have been associated to hematologic malignancies. More recently, biallelic, and monoallelic germline mutations conferring susceptibility to lymphoid and myeloid cancer have been described. We report two unrelated autoimmune lymphoproliferative syndrome-like patients who presented with T-cell lymphoma associated with novel germline biallelic or monoallelic mutations in the TET2 gene. Both patients presented a history of chronic lymphoproliferation with lymphadenopathies and splenomegaly, cytopenias, and immune dysregulation. We identified the first compound heterozygous patient for TET2 mutations (P1) and the first ALPS-like patient with a monoallelic TET2 mutation (P2). P1 had the most severe form of autosomal recessive disease due to TET2 loss of function resulting in absent TET2 expression and profound increase in DNA methylation. Additionally, the immunophenotype showed some alterations in innate and adaptive immune system as inverted myeloid/plasmacytoid dendritic cells ratio, elevated terminally differentiated effector memory CD8 + T-cells re-expressing CD45RA, regulatory T-cells, and Th2 circulating follicular T-cells. Double-negative T-cells, vitamin B12, and IL-10 were elevated according to the ALPS-like suspicion. Interestingly, the healthy P1's brother carried a TET2 mutation and presented some markers of immune dysregulation. P2 showed elevated vitamin B12, hypergammaglobulinemia, and decreased HDL levels. Therefore, novel molecular defects in TET2 confirm and expand both clinical and immunological phenotype, contributing to a better knowledge of the bridge between cancer and immunity.
Collapse
Affiliation(s)
- Marta López-Nevado
- Immunology Department, University Hospital 12 de Octubre, Av de Córdoba s/n, 28041, Madrid, Spain.
- Research Institute Hospital 12 de Octubre (imas12), Madrid, Spain.
| | | | - Cristina Serrano
- Immunology Department, University Hospital Fundación Jiménez Díaz, Madrid, Spain
| | - María A Pérez-Saez
- Hematology Department, University Hospital Fundación Jiménez Díaz, Madrid, Spain
| | - José L López-Lorenzo
- Hematology Department, University Hospital Fundación Jiménez Díaz, Madrid, Spain
| | - Francisco J Gil-Etayo
- Immunology Department, University Hospital 12 de Octubre, Av de Córdoba s/n, 28041, Madrid, Spain
- Research Institute Hospital 12 de Octubre (imas12), Madrid, Spain
| | - Edgar Rodríguez-Frías
- Immunology Department, University Hospital 12 de Octubre, Av de Córdoba s/n, 28041, Madrid, Spain
- Research Institute Hospital 12 de Octubre (imas12), Madrid, Spain
| | - Oscar Cabrera-Marante
- Immunology Department, University Hospital 12 de Octubre, Av de Córdoba s/n, 28041, Madrid, Spain
- Research Institute Hospital 12 de Octubre (imas12), Madrid, Spain
| | - Pablo Morales-Pérez
- Immunology Department, University Hospital 12 de Octubre, Av de Córdoba s/n, 28041, Madrid, Spain
- Research Institute Hospital 12 de Octubre (imas12), Madrid, Spain
| | | | - Rebeca Manso
- Pathology Department, Research Institute Fundación Jiménez Díaz, Madrid, Spain
| | | | - Ana Cerdá-Montagud
- Hematology Department, University Hospital Fundación Jiménez Díaz, Madrid, Spain
| | - Juan F Quesada-Espinosa
- Genetics Department, University Hospital 12 de Octubre, Madrid, Spain
- UDisGen (Unidad de Dismorfología Y Genética), University Hospital 12 de Octubre, Madrid, Spain
| | - María J Gómez-Rodríguez
- Genetics Department, University Hospital 12 de Octubre, Madrid, Spain
- UDisGen (Unidad de Dismorfología Y Genética), University Hospital 12 de Octubre, Madrid, Spain
| | - Estela Paz-Artal
- Immunology Department, University Hospital 12 de Octubre, Av de Córdoba s/n, 28041, Madrid, Spain
- Research Institute Hospital 12 de Octubre (imas12), Madrid, Spain
- School of Medicine, Complutense University of Madrid, Madrid, Spain
- CIBERINFEC, ISCIII, Madrid, Spain
| | - Cecilia Muñoz-Calleja
- Immunology Department, University Hospital La Princesa, Madrid, Spain
- School of Medicine, University Autónoma de Madrid, Madrid, Spain
- Research Institute Hospital de La Princesa, Madrid, Spain
| | - Reyes Arranz-Sáez
- Hematology Department, University Hospital La Princesa, Madrid, Spain
| | - Luis M Allende
- Immunology Department, University Hospital 12 de Octubre, Av de Córdoba s/n, 28041, Madrid, Spain.
- Research Institute Hospital 12 de Octubre (imas12), Madrid, Spain.
- School of Medicine, Complutense University of Madrid, Madrid, Spain.
| |
Collapse
|
32
|
Singh SM, Win PW, Castellani CA. Complementary approaches involving monozygotic twins and single neuron genomics support postzygotic somatic mutations in schizophrenia. Schizophr Res 2022; 248:228-230. [PMID: 36108467 DOI: 10.1016/j.schres.2022.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 08/05/2022] [Accepted: 09/04/2022] [Indexed: 10/14/2022]
Affiliation(s)
- S M Singh
- Department of Biology, Western University, London, Canada
| | - P W Win
- Department of Biology, Western University, London, Canada; Department of Pathology and Laboratory Medicine, Western University, London, Canada
| | - C A Castellani
- Department of Pathology and Laboratory Medicine, Western University, London, Canada; Department of Epidemiology and Biostatistics, Western University, London, Canada.
| |
Collapse
|
33
|
Pudjihartono M, Perry JK, Print C, O'Sullivan JM, Schierding W. Interpretation of the role of germline and somatic non-coding mutations in cancer: expression and chromatin conformation informed analysis. Clin Epigenetics 2022; 14:120. [PMID: 36171609 PMCID: PMC9520844 DOI: 10.1186/s13148-022-01342-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 09/21/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There has been extensive scrutiny of cancer driving mutations within the exome (especially amino acid altering mutations) as these are more likely to have a clear impact on protein functions, and thus on cell biology. However, this has come at the neglect of systematic identification of regulatory (non-coding) variants, which have recently been identified as putative somatic drivers and key germline risk factors for cancer development. Comprehensive understanding of non-coding mutations requires understanding their role in the disruption of regulatory elements, which then disrupt key biological functions such as gene expression. MAIN BODY We describe how advancements in sequencing technologies have led to the identification of a large number of non-coding mutations with uncharacterized biological significance. We summarize the strategies that have been developed to interpret and prioritize the biological mechanisms impacted by non-coding mutations, focusing on recent annotation of cancer non-coding variants utilizing chromatin states, eQTLs, and chromatin conformation data. CONCLUSION We believe that a better understanding of how to apply different regulatory data types into the study of non-coding mutations will enhance the discovery of novel mechanisms driving cancer.
Collapse
Affiliation(s)
| | - Jo K Perry
- Liggins Institute, The University of Auckland, Auckland, New Zealand
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
| | - Cris Print
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
- Department of Molecular Medicine and Pathology, School of Medical Sciences, University of Auckland, Auckland, 1142, New Zealand
| | - Justin M O'Sullivan
- Liggins Institute, The University of Auckland, Auckland, New Zealand
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
- Australian Parkinson's Mission, Garvan Institute of Medical Research, Sydney, NSW, Australia
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
| | - William Schierding
- Liggins Institute, The University of Auckland, Auckland, New Zealand.
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand.
| |
Collapse
|
34
|
Antra, Parashar P, Hungyo H, Jain A, Ahmad S, Tandon V. Unraveling molecular mechanisms of Head and neck cancer. Crit Rev Oncol Hematol 2022; 178:103778. [PMID: 35932993 DOI: 10.1016/j.critrevonc.2022.103778] [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: 07/26/2021] [Revised: 03/02/2022] [Accepted: 08/01/2022] [Indexed: 12/24/2022] Open
Abstract
Malignancies that develop from mucosal epithelium of the upper aerodigestive tract are known as head and neck squamous cell carcinomas (HNSCC). Heterogeneity, late stage diagnosis and high recurrence rate are big hurdles in head and neck treatment regimen. Presently, the biomarkers available for diagnosis and prognosis of HNSCC are based on smoking as the major risk habit. This review shed light on the differential environment of HNSCC in smokeless tobacco consuming Indian patients. Frequent mutation in genes involved in DNA repair pathway (p53), cell proliferation (PIK3CA, HRAS) and cell death (CASP8, FADD) are common in western population. On the contrary, the genes involved in metastasis (MMPs, YAP1), lymphocyte proliferation (TNFRSF4, CD80), cell-cell adhesion (DCC, EDNRB), miRNA processing (DROSHA) and inflammatory responses (TLR9, IL-9) are mutated in Indian HNSCC patients. Gene ontology enrichment analysis highlighted that responses to chemical stimulus, immune pathways and stress pathways are highly enriched in Indian patients.
Collapse
Affiliation(s)
- Antra
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067
| | - Palak Parashar
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067
| | - Hungharla Hungyo
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067
| | - Anuja Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067
| | - Shandar Ahmad
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067
| | - Vibha Tandon
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067.
| |
Collapse
|
35
|
Wang C, Shi J, Cai J, Zhang Y, Zheng X, Zhang N. DriverRWH: discovering cancer driver genes by random walk on a gene mutation hypergraph. BMC Bioinformatics 2022; 23:277. [PMID: 35831792 PMCID: PMC9281118 DOI: 10.1186/s12859-022-04788-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 06/08/2022] [Indexed: 12/24/2022] Open
Abstract
Background Recent advances in next-generation sequencing technologies have helped investigators generate massive amounts of cancer genomic data. A critical challenge in cancer genomics is identification of a few cancer driver genes whose mutations cause tumor growth. However, the majority of existing computational approaches underuse the co-occurrence mutation information of the individuals, which are deemed to be important in tumorigenesis and tumor progression, resulting in high rate of false positive. Results To make full use of co-mutation information, we present a random walk algorithm referred to as DriverRWH on a weighted gene mutation hypergraph model, using somatic mutation data and molecular interaction network data to prioritize candidate driver genes. Applied to tumor samples of different cancer types from The Cancer Genome Atlas, DriverRWH shows significantly better performance than state-of-art prioritization methods in terms of the area under the curve scores and the cumulative number of known driver genes recovered in top-ranked candidate genes. Besides, DriverRWH discovers several potential drivers, which are enriched in cancer-related pathways. DriverRWH recovers approximately 50% known driver genes in the top 30 ranked candidate genes for more than half of the cancer types. In addition, DriverRWH is also highly robust to perturbations in the mutation data and gene functional network data. Conclusion DriverRWH is effective among various cancer types in prioritizes cancer driver genes and provides considerable improvement over other tools with a better balance of precision and sensitivity. It can be a useful tool for detecting potential driver genes and facilitate targeted cancer therapies. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04788-7.
Collapse
Affiliation(s)
- Chenye Wang
- School of Mathematics and Statistics, Shandong University, Weihai, 264209, China
| | - Junhan Shi
- School of Mathematics and Statistics, Shandong University, Weihai, 264209, China
| | - Jiansheng Cai
- Department of Mathematics, Weifang University, Weifang, 261061, Shandong, China
| | - Yusen Zhang
- School of Mathematics and Statistics, Shandong University, Weihai, 264209, China
| | - Xiaoqi Zheng
- Department of Mathematics, Shanghai Normal University, Shanghai, 200234, China
| | - Naiqian Zhang
- School of Mathematics and Statistics, Shandong University, Weihai, 264209, China.
| |
Collapse
|
36
|
Wasilewska K, Gambin T, Rydzanicz M, Szczałuba K, Płoski R. Postzygotic mutations and where to find them - Recent advances and future implications in the field of non-neoplastic somatic mosaicism. Mutat Res Rev Mutat Res 2022; 790:108426. [PMID: 35690331 DOI: 10.1016/j.mrrev.2022.108426] [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] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 05/05/2022] [Accepted: 06/03/2022] [Indexed: 01/01/2023]
Abstract
The technological progress of massively parallel sequencing (MPS) has triggered a remarkable development in the research on postzygotic mutations. Although the overwhelming majority of studies in the field focus on oncogenesis, non-neoplastic diseases are attracting more and more attention. The aim of this review was to summarize some of the most recent findings in the field of somatic mosaicism in diseases other than neoplastic events. We discuss the abundance and role of postzygotic mutations, with a special emphasis on disorders which occur only in a mosaic form (obligatory mosaic diseases; OMDs). Based on the list of OMDs compiled from the published literature and three databases (OMIM, Orphanet and MosaicBase), we demonstrate the prevalence of cancer-related genes across OMDs and suggest other sources to further explore OMDs and OMD-related genes. Additionally, we comment on some practical aspects related to mosaic diseases, such as approaches to tissue sampling, the MPS coverage required to detect variants at a very low frequency, as well as on bioinformatic and molecular tools dedicated to detect somatic mutations in MPS data.
Collapse
Affiliation(s)
- Krystyna Wasilewska
- Department of Medical Genetics, Medical University of Warsaw, ul. Pawińskiego 3c, 02-106 Warsaw, Poland
| | - Tomasz Gambin
- Institute of Computer Science, Warsaw University of Technology, Nowowiejska 15/19, 00-665 Warsaw, Poland
| | - Małgorzata Rydzanicz
- Department of Medical Genetics, Medical University of Warsaw, ul. Pawińskiego 3c, 02-106 Warsaw, Poland
| | - Krzysztof Szczałuba
- Department of Medical Genetics, Medical University of Warsaw, ul. Pawińskiego 3c, 02-106 Warsaw, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, ul. Pawińskiego 3c, 02-106 Warsaw, Poland.
| |
Collapse
|
37
|
Cruces MP, González E, Pimentel E, Jiménez E, Sánchez P. Relationship between lifespan and somatic mutation in D. melanogaster after treatment with chlorophyllin. Environ Toxicol Pharmacol 2022; 93:103891. [PMID: 35654371 DOI: 10.1016/j.etap.2022.103891] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 05/06/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
Sodium copper chlorophyllin (SCC) has a genetic damage inhibitory capacity due to its antioxidant action. For this reason, it was considered to investigate its role in the life span of Drosophila melanogaster and its relationship with the frequency of somatic mutation induced by gamma rays. Results indicated that SCC alone prolonged the lifespan only in females, but in combination with 20 Gy of gamma rays, the aging delay in both sexes was significant. In addition to confirming that the porphyrin reduces the frequency of mutation, the individuals with the highest mutation load are the individuals who die more quickly, and once they are eliminated, the survivor individuals treated with 20 Gy or with SCC + 20 Gy, died at the same rate. The results together indicate that SCC not only inhibits induced genetic damage, but it also has beneficial effects that probably cause an aging delay of the treated population that need to be investigated.
Collapse
Affiliation(s)
- Martha Patricia Cruces
- Departamento de Biología, Instituto Nacional de Investigaciones Nucleares (ININ), Carretera México-Toluca, S/N, la Marquesa, Ocoyoacac CP. 52750, México
| | - Elena González
- Departamento de Biología, Instituto Nacional de Investigaciones Nucleares (ININ), Carretera México-Toluca, S/N, la Marquesa, Ocoyoacac CP. 52750, México
| | - Emilio Pimentel
- Departamento de Biología, Instituto Nacional de Investigaciones Nucleares (ININ), Carretera México-Toluca, S/N, la Marquesa, Ocoyoacac CP. 52750, México.
| | - Elizabeth Jiménez
- Departamento de Biología, Instituto Nacional de Investigaciones Nucleares (ININ), Carretera México-Toluca, S/N, la Marquesa, Ocoyoacac CP. 52750, México
| | - Petra Sánchez
- Facultad de Ciencias, Universidad Autónoma del Estado de México, Toluca, Edo Mex., México
| |
Collapse
|
38
|
Hu K, Wang C, Luo C, Zheng H, Song H, Bergstedt J, Fall K, Luo T, Czene K, Valdimarsdóttir UA, Fang F, Lu D. Neuroendocrine pathways and breast cancer progression: a pooled analysis of somatic mutations and gene expression from two large breast cancer cohorts. BMC Cancer 2022; 22:680. [PMID: 35729536 PMCID: PMC9210628 DOI: 10.1186/s12885-022-09779-8] [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: 02/11/2022] [Accepted: 06/15/2022] [Indexed: 02/08/2023] Open
Abstract
Background Experimental studies indicate that neuroendocrine pathways might play a role in progression of breast cancer. We aim to test the hypothesis that somatic mutations in the genes of neuroendocrine pathways influence breast cancer prognosis, through dysregulated gene expression in tumor tissue. Methods We conducted an extreme case–control study including 208 breast cancer patients with poor invasive disease-free survival (iDFS) and 208 patients with favorable iDFS who were individually matched on molecular subtype from the Breast Cancer Cohort at West China Hospital (WCH; N = 192) and The Cancer Genome Atlas (TCGA; N = 224). Whole exome sequencing and RNA sequencing of tumor and paired normal breast tissues were performed. Adrenergic, glucocorticoid, dopaminergic, serotonergic, and cholinergic pathways were assessed for differences in mutation burden and gene expression in relation to breast cancer iDFS using the logistic regression and global test, respectively. Results In the pooled analysis, presence of any somatic mutation (odds ratio = 1.66, 95% CI: 1.07–2.58) of the glucocorticoid pathway was associated with poor iDFS and a two-fold increase of tumor mutation burden was associated with 17% elevated odds (95% CI: 2–35%), after adjustment for cohort membership, age, menopausal status, molecular subtype, and tumor stage. Differential expression of genes in the glucocorticoid pathway in tumor tissue (P = 0.028), but not normal tissue (P = 0.701), was associated with poor iDFS. Somatic mutation of the adrenergic and cholinergic pathways was significantly associated with iDFS in WCH, but not in TCGA. Conclusion Glucocorticoid pathway may play a role in breast cancer prognosis through differential mutations and expression. Further characterization of its functional role may open new avenues for the development of novel therapeutic targets for breast cancer. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09779-8.
Collapse
Affiliation(s)
- Kejia Hu
- Laboratory of Molecular Diagnosis of Cancer, Clinical Research Center for Breast, West China Hospital, Sichuan University, Chengdu, China.,Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Chengshi Wang
- Laboratory of Molecular Diagnosis of Cancer, Clinical Research Center for Breast, West China Hospital, Sichuan University, Chengdu, China.,Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Chuanxu Luo
- Laboratory of Molecular Diagnosis of Cancer, Clinical Research Center for Breast, West China Hospital, Sichuan University, Chengdu, China
| | - Hong Zheng
- Laboratory of Molecular Diagnosis of Cancer, Clinical Research Center for Breast, West China Hospital, Sichuan University, Chengdu, China
| | - Huan Song
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, China.,Center of Public Health Sciences, Faculty of Medicine, University of Iceland, Reykjavík, Iceland
| | - Jacob Bergstedt
- Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Katja Fall
- Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Clinical Epidemiology and Biostatistics, School of Medical Sciences, Örebro Universitet, Örebro, Sweden
| | - Ting Luo
- Laboratory of Molecular Diagnosis of Cancer, Clinical Research Center for Breast, West China Hospital, Sichuan University, Chengdu, China
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Unnur A Valdimarsdóttir
- Center of Public Health Sciences, Faculty of Medicine, University of Iceland, Reykjavík, Iceland.,Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Fang Fang
- Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Donghao Lu
- Laboratory of Molecular Diagnosis of Cancer, Clinical Research Center for Breast, West China Hospital, Sichuan University, Chengdu, China. .,Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden. .,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| |
Collapse
|
39
|
Kwon SG, Bae GH, Choi JH, Mali NM, Jun MS, Kim DS, Han MH, Park S, Ju YS, Choi SH, Oh JW. Asymmetric Contribution of Blastomere Lineages of First Division of the Zygote to Entire Human Body Using Post-Zygotic Variants. Tissue Eng Regen Med 2022. [PMID: 35438457 DOI: 10.1007/s13770-022-00443-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/02/2022] [Accepted: 02/13/2022] [Indexed: 10/18/2022] Open
Abstract
BACKGROUND In humans, after fertilization, the zygote divides into two 2n diploid daughter blastomeres. During this division, DNA is replicated, and the remaining mutually exclusive genetic mutations in the genome of each cell are called post-zygotic variants. Using these somatic mutations, developmental lineages can be reconstructed. How these two blastomeres are contributing to the entire body is not yet identified. This study aims to evaluate the cellular contribution of two blastomeres of 2-cell embryos to the entire body in humans using post-zygotic variants based on whole genome sequencing. METHODS Tissues from different anatomical areas were obtained from five donated cadavers for use in single-cell clonal expansion and bulk target sequencing. After conducting whole genome sequencing, computational analysis was applied to find the early embryonic mutations of each clone. We developed our in-house bioinformatics pipeline, and filtered variants using strict criteria, composed of mapping quality, base quality scores, depth, soft-clipped reads, and manual inspection, resulting in the construction of embryological phylogenetic cellular trees. RESULTS Using our in-house pipeline for variant filtering, we could extract accurate true positive variants, and construct the embryological phylogenetic trees for each cadaver. We found that two daughter blastomeres, L1 and L2 (lineage 1 and 2, respectively), derived from the zygote, distribute unequally to the whole body at the clonal level. From bulk target sequencing data, we validated asymmetric contribution by means of the variant allele frequency of L1 and L2. The asymmetric contribution of L1 and L2 varied from person to person. CONCLUSION We confirmed that there is asymmetric contribution of two daughter blastomeres from the first division of the zygote across the whole human body.
Collapse
|
40
|
Nishioka Y, Paez-Arango N, Boettcher FO, Kawaguchi Y, Newhook TE, Chun YS, Tzeng CWD, Tran Cao HS, Lee JE, Vreeland TJ, Vauthey JN. Neither Surgical Margin Status nor Somatic Mutation Predicts Local Recurrence After R0-intent Resection for Colorectal Liver Metastases. J Gastrointest Surg 2022; 26:791-801. [PMID: 34725784 DOI: 10.1007/s11605-021-05173-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 06/24/2021] [Accepted: 09/04/2021] [Indexed: 01/31/2023]
Abstract
BACKGROUND We evaluated the associations of surgical margin status and somatic mutations with the incidence of local recurrence (LR) and oncologic outcomes in patients undergoing R0-intent (microscopically negative margin) resection of colorectal liver metastases (CLM). METHODS Patients with CLM who underwent initial R0-intent resection and analysis of tumor tissue using next-generation sequencing during 2001-2018 were analyzed. Recurrences were classified as LR (at the resection margin), other intrahepatic recurrence, or extrahepatic recurrence. Predictors and survival effect of LR were evaluated using univariate and multivariate analysis. RESULTS Of 552 patients analyzed, 415 (75%) had R0 resection (margin width ≥ 1.0 mm), and 38 (7%) had LR. LR incidence was not affected by surgical margin width. RAS/TP53 co-mutation was associated with increased risk of intrahepatic recurrence (67% vs. 49%; p < 0.001) and overall recurrence (p < 0.001). However, incidence of LR did not differ significantly by RAS/TP53, BRAF, SMAD4, or FBXW7 mutation. Extrahepatic disease (hazard ratio [HR], 1.47; p = 0.034), > 8 cycles of preoperative chemotherapy (HR, 1.98; p = 0.033), tumor viability ≥ 50% (HR, 1.55; p = 0.007), RAS/TP53 co-mutation (HR, 1.69; p = 0.001), and SMAD4 mutation (HR, 2.44; p < 0.001) were independently associated with poor overall survival, but surgical margin status was not. CONCLUSIONS Although somatic mutations were associated with overall recurrence, neither surgical margin width nor somatic mutations affected LR risk after R0-intent hepatectomy for CLM. LR and prognosis were likely driven by individual tumor biology rather than surgical margins.
Collapse
Affiliation(s)
- Yujiro Nishioka
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 1484, Houston, TX, 77030, USA
| | - Natalia Paez-Arango
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 1484, Houston, TX, 77030, USA
| | - Federico Oppliger Boettcher
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 1484, Houston, TX, 77030, USA
| | - Yoshikuni Kawaguchi
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 1484, Houston, TX, 77030, USA.,Hepato-Biliary-Pancreatic Surgery Division, Department of Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Timothy E Newhook
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 1484, Houston, TX, 77030, USA
| | - Yun Shin Chun
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 1484, Houston, TX, 77030, USA
| | - Ching-Wei D Tzeng
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 1484, Houston, TX, 77030, USA
| | - Hop S Tran Cao
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 1484, Houston, TX, 77030, USA
| | - Jeffrey E Lee
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 1484, Houston, TX, 77030, USA
| | - Timothy J Vreeland
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 1484, Houston, TX, 77030, USA.,Department of Surgery, Brooke Army Medical Center, Ft. Sam Houston, San Antonio, TX, USA
| | - Jean-Nicolas Vauthey
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 1484, Houston, TX, 77030, USA.
| |
Collapse
|
41
|
Law SM, Akizuki S, Morinobu A, Ohmura K. A case of refractory systemic lupus erythematosus with monocytosis exhibiting somatic KRAS mutation. Inflamm Regen 2022; 42:10. [PMID: 35361277 PMCID: PMC8973904 DOI: 10.1186/s41232-022-00195-w] [Citation(s) in RCA: 2] [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: 11/08/2021] [Accepted: 01/20/2022] [Indexed: 11/11/2022] Open
Abstract
Background Systemic lupus erythematosus (SLE), an autoimmune disorder that damages various organ systems, is caused by a combination of genetic and environmental factors. Although germline mutations of several genes are known to cause juvenile SLE, most of the susceptibility genetic variants of adult SLE are common variants of the population, somatic mutations that cause or exacerbate SLE have not been reported. We hereby report a refractory SLE case with monocytosis accompanying somatic KRAS mutation that have been shown to cause lupus-like symptoms. Case presentation A 60-year-old female patient who had been diagnosed with SLE was admitted to our hospital. Although prednisolone and tacrolimus treatments had kept her thrombocytopenia and anti-DNA Ab level at bay for more than 4 years, a diagnosis of transverse myelitis was made when she became acutely ill with pleocytosis. Elevated cells (predominately monocytes), protein, IgG, and IL-6 levels were also found in the cerebrospinal fluid (CSF) of the patient. Standard pulse treatments of methylprednisolone, high-dose of prednisolone, and intravenous cyclophosphamide in combination with plasma exchange could not alleviate the refractory neural and autoimmune manifestation. Monocytosis of peripheral blood was also noted. Flow cytometric analysis revealed elevated ratio of CD14+CD16+ atypical monocytes, which excluded the possibility of chronic myelomonocytic leukemia. Lupus-like symptoms with monocytosis reminded us of Ras-associated autoimmune leukoproliferative disorder, and Sanger sequencing of KRAS and NRAS genes from the patients’ peripheral blood mononuclear cells (PBMC), sorted CD3+ lymphocytes and CD14+ monocytes, and cerebrospinal fluid were performed. An activating KRAS somatic mutation was found in the patients’ DNA at the time of encephalomyelitis diagnosis. Conclusion Somatic mutations of some genes including KRAS may cause the refractoriness of SLE.
Collapse
Affiliation(s)
- Sze-Ming Law
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, 54 kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Shuji Akizuki
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, 54 kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Akio Morinobu
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, 54 kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Koichiro Ohmura
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, 54 kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan. .,Department of Rheumatology, Kobe City Medical Center General Hospital, Kobe, Japan.
| |
Collapse
|
42
|
Wang D, Zhang Y, li R, Li J, Zhang R. Consistency and reproducibility of large panel next-generation sequencing: Multi-laboratory assessment of somatic mutation detection on reference materials with mismatch repair and proofreading deficiency. J Adv Res 2022; 44:161-172. [PMID: 36725187 PMCID: PMC9937796 DOI: 10.1016/j.jare.2022.03.016] [Citation(s) in RCA: 2] [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: 12/24/2021] [Revised: 03/16/2022] [Accepted: 03/27/2022] [Indexed: 02/04/2023] Open
Abstract
INTRODUCTION Clinical precision oncology increasingly relies on accurate genome-wide profiling using large panel next generation sequencing; however, difficulties in accurate and consistent detection of somatic mutation from individual platforms and pipelines remain an open question. OBJECTIVES To obtain paired tumor-normal reference materials that can be effectively constructed and interchangeable with clinical samples, and evaluate the performance of 56 panels under routine testing conditions based on the reference samples. METHODS Genes involved in mismatch repair and DNA proofreading were knocked down using the CRISPR-Cas9 technology to accumulate somatic mutations in a defined GM12878 cell line. They were used as reference materials to comprehensively evaluate the reproducibility and accuracy of detection results of oncopanels and explore the potential influencing factors. RESULTS In total, 14 paired tumor-normal reference DNA samples from engineered cell lines were prepared, and a reference dataset comprising 168 somatic mutations in a high-confidence region of 1.8 Mb were generated. For mutations with an allele frequency (AF) of more than 5% in reference samples, 56 panels collectively reported 1306 errors, including 729 false negatives (FNs), 179 false positives (FPs) and 398 reproducibility errors. The performance metric varied among panels with precision and recall ranging from 0.773 to 1 and 0.683 to 1, respectively. Incorrect and inadequate filtering accounted for a large proportion of false discovery (including FNs and FPs), while low-quality detection, cross-contamination and other sequencing errors during the wet bench process were other sources of FNs and FPs. In addition, low AF (<5%) considerably influenced the reproducibility and comparability among panels. CONCLUSIONS This study provided an integrated practice for developing reference standard to assess oncopanels in detecting somatic mutations and quantitatively revealed the source of detection errors. It will promote optimization, validation, and quality control among laboratories with potential applicability in clinical use.
Collapse
Affiliation(s)
- Duo Wang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P. R. China,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China
| | - Yuanfeng Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P. R. China,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China
| | - Rui li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P. R. China,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P. R. China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China.
| | - Rui Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P. R. China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China.
| |
Collapse
|
43
|
Zhang X, Wang Y, Meng L. Comparative genomic analysis of esophageal squamous cell carcinoma and adenocarcinoma: New opportunities towards molecularly targeted therapy. Acta Pharm Sin B 2022; 12:1054-1067. [PMID: 35530133 PMCID: PMC9069403 DOI: 10.1016/j.apsb.2021.09.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/23/2021] [Accepted: 08/27/2021] [Indexed: 12/12/2022] Open
Abstract
Esophageal cancer is one of the most lethal cancers worldwide because of its rapid progression and poor prognosis. Esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EAC) are two major subtypes of esophageal cancer. ESCC predominantly affects African and Asian populations, which is closely related to chronic smoking and alcohol consumption. EAC typically arises in Barrett's esophagus with a predilection for Western countries. While surgical operation and chemoradiotherapy have been applied to combat this deadly cancer, molecularly targeted therapy is still at the early stages. With the development of large-scale next-generation sequencing, various genomic alterations in ESCC and EAC have been revealed and their potential roles in the initiation and progression of esophageal cancer have been studied. Potential therapeutic targets have been identified and novel approaches have been developed to combat esophageal cancer. In this review, we comprehensively analyze the genomic alterations in EAC and ESCC and summarize the potential role of the genetic alterations in the development of esophageal cancer. Progresses in the therapeutics based on the different tissue types and molecular signatures have also been reviewed and discussed.
Collapse
|
44
|
Abstract
The VEXAS syndrome is a recently identified autoinflammatory systemic disease. The acronym VEXAS stands for Vacuoles, E1 enzyme, X‑linked, Autoinflammatory, Somatic. The disease is due to an acquired somatic mutation of the UBA1 gene, which encodes for the E‑1 enzyme, which in turn is responsible for the ubiquitination of proteins. Due to its location on the X chromosome, the disease predominantly affects men (in the second half of life). The patients present with a plethora of inflammatory clinical symptoms, often with overlap of hematologic, dermatologic, and rheumatologic syndromes. In particular, the presence of cytoplasmic vacuoles in the bone marrow is characteristic. In this article we report the clinical case of a VEXAS patient and give an overview of the pathophysiology, clinical symptoms and diagnostics of the disease.
Collapse
Affiliation(s)
- M Zeeck
- Sektion für Rheumatologie und Entzündliche Systemerkrankungen, Universitätsklinikum Hamburg-Eppendorf (UKE), Martinistr. 52, 20246, Hamburg, Deutschland
- Klinik für Rheumatologie und Immunologie, Bad Bramstedt, Deutschland
| | - I Kötter
- Sektion für Rheumatologie und Entzündliche Systemerkrankungen, Universitätsklinikum Hamburg-Eppendorf (UKE), Martinistr. 52, 20246, Hamburg, Deutschland
- Klinik für Rheumatologie und Immunologie, Bad Bramstedt, Deutschland
| | - M Krusche
- Sektion für Rheumatologie und Entzündliche Systemerkrankungen, Universitätsklinikum Hamburg-Eppendorf (UKE), Martinistr. 52, 20246, Hamburg, Deutschland.
| |
Collapse
|
45
|
Liu Y, Gusev A, Heng YJ, Alexandrov LB, Kraft P. Somatic mutational profiles and germline polygenic risk scores in human cancer. Genome Med 2022; 14:14. [PMID: 35144655 PMCID: PMC8832866 DOI: 10.1186/s13073-022-01016-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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: 04/01/2021] [Accepted: 01/24/2022] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND The mutational profile of cancer reflects the activity of the mutagenic processes which have been operative throughout the lineage of the cancer cell. These processes leave characteristic profiles of somatic mutations called mutational signatures. Mutational signatures, including single-base substitution (SBS) signatures, may reflect the effects of exogenous or endogenous exposures. METHODS We used polygenic risk scores (PRS) to summarize common germline variation associated with cancer risk and other cancer-related traits and examined the association between somatic mutational profiles and germline PRS in 12 cancer types from The Cancer Genome Atlas. Somatic mutational profiles were constructed from whole-exome sequencing data of primary tumors. PRS were calculated for the 12 selected cancer types and 9 non-cancer traits, including cancer risk determinants, hormonal factors, and immune-mediated inflammatory diseases, using germline genetic data and published summary statistics from genome-wide association studies. RESULTS We found 17 statistically significant associations between somatic mutational profiles and germline PRS after Bonferroni correction (p < 3.15 × 10-5), including positive associations between germline inflammatory bowel disease PRS and number of somatic mutations attributed to signature SBS1 in prostate cancer and APOBEC-related signatures in breast cancer. Positive associations were also found between age at menarche PRS and mutation counts of SBS1 in overall and estrogen receptor-positive breast cancer. Consistent with prior studies that found an inverse association between the pubertal development PRS and risk of prostate cancer, likely reflecting hormone-related mechanisms, we found an inverse association between age at menarche PRS and mutation counts of SBS1 in prostate cancer. Inverse associations were also found between several cancer PRS and tumor mutation counts. CONCLUSIONS Our analysis suggests that there are robust associations between tumor somatic mutational profiles and germline PRS. These may reflect the mechanisms through hormone regulation and immune responses that contribute to cancer etiology and drive cancer progression.
Collapse
Affiliation(s)
- Yuxi Liu
- grid.38142.3c000000041936754XDepartment of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115 USA ,grid.38142.3c000000041936754XProgram in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Boston, MA 02115 USA
| | - Alexander Gusev
- grid.65499.370000 0001 2106 9910Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215 USA
| | - Yujing J. Heng
- grid.38142.3c000000041936754XDepartment of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215 USA
| | - Ludmil B. Alexandrov
- grid.266100.30000 0001 2107 4242Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093 USA
| | - Peter Kraft
- grid.38142.3c000000041936754XDepartment of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115 USA ,grid.38142.3c000000041936754XProgram in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Boston, MA 02115 USA ,grid.38142.3c000000041936754XDepartment of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115 USA
| |
Collapse
|
46
|
Stuckey R, López Rodríguez JF, Gómez-Casares MT. Discontinuation of Tyrosine Kinase Inhibitors in Patients with Chronic Myeloid Leukemia: a Review of the Biological Factors Associated with Treatment-Free Remission. Curr Oncol Rep 2022; 24:415-426. [PMID: 35141859 PMCID: PMC8930955 DOI: 10.1007/s11912-022-01228-w] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2021] [Indexed: 11/30/2022]
Abstract
Purpose of Review Clinical factors alone do not enable us to differentiate which patients will maintain treatment-free remission (TFR) from those who are likely to relapse. Thus, patient-specific factors must also play a role. This review will update the reader on the most recent studies presenting biological factors that can help predict tyrosine kinase inhibitor (TKI) discontinuation success. Recent Findings Cellular and molecular factors with a suggested role in TFR include immune factors and leukemic stem cell (LSC) persistence; the BCR::ABL1 transcript type, halving time, and BCR::ABL1 DNA and RNA positivity; as well as other molecular factors such as somatic mutations, RNA expression, and telomere length. Summary Our review presents several biomarkers with predictive value for TFR but also highlights areas of unmet need. Future discontinuation guidelines will likely include biological factors for the personalization of TFR prediction. However, it will be important that such advances do not prevent more patients from making a TKI discontinuation attempt.
Collapse
Affiliation(s)
- Ruth Stuckey
- Hematology Department, Hospital Universitario de Gran Canaria Dr. Negrín, Barranco de la Ballena s/n, Las Palmas, Spain.
| | | | - María Teresa Gómez-Casares
- Hematology Department, Hospital Universitario de Gran Canaria Dr. Negrín, Barranco de la Ballena s/n, Las Palmas, Spain
- Medical Science Department, Universidad de Las Palmas de Gran Canaria, Las Palmas, Spain
| |
Collapse
|
47
|
Grillo E, Ravelli C, Corsini M, Gaudenzi C, Zammataro L, Mitola S. Novel potential oncogenic and druggable mutations of FGFRs recur in the kinase domain across cancer types. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166313. [PMID: 34826586 DOI: 10.1016/j.bbadis.2021.166313] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 12/19/2022]
Abstract
Fibroblast growth factor receptors (FGFRs) are recurrently altered by single nucleotide variants (SNVs) in many human cancers. The prevalence of SNVs in FGFRs depends on the cancer type. In some tumors, such as the urothelial carcinoma, mutations of FGFRs occur at very high frequency (up to 60%). Many characterized mutations occur in the extracellular or transmembrane domains, while fewer known mutations are found in the kinase domain. In this study, we performed a bioinformatics analysis to identify novel putative cancer driver or therapeutically actionable mutations of the kinase domain of FGFRs. To pinpoint those mutations that may be clinically relevant, we exploited the recurrence of alterations on analogous amino acid residues within the kinase domain (PK_Tyr_Ser-Thr) of different kinases as a predictor of functional impact. By exploiting MutationAligner and LowMACA bioinformatics resources, we highlighted novel uncharacterized mutations of FGFRs which recur in other protein kinases. By revealing unanticipated correspondence with known variants, we were able to infer their functional effects, as alterations clustering on similar residues in analogous proteins have a high probability to elicit similar effects. As FGFRs represent an important class of oncogenes and drug targets, our study opens the way for further studies to validate their driver and/or actionable nature and, in the long term, for a more efficacious application of precision oncology.
Collapse
|
48
|
Sahraeian SME, Fang LT, Karagiannis K, Moos M, Smith S, Santana-Quintero L, Xiao C, Colgan M, Hong H, Mohiyuddin M, Xiao W. Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample. Genome Biol 2022; 23:12. [PMID: 34996510 PMCID: PMC8740374 DOI: 10.1186/s13059-021-02592-9] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 12/28/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Accurate detection of somatic mutations is challenging but critical in understanding cancer formation, progression, and treatment. We recently proposed NeuSomatic, the first deep convolutional neural network-based somatic mutation detection approach, and demonstrated performance advantages on in silico data. RESULTS In this study, we use the first comprehensive and well-characterized somatic reference data sets from the SEQC2 consortium to investigate best practices for using a deep learning framework in cancer mutation detection. Using the high-confidence somatic mutations established for a cancer cell line by the consortium, we identify the best strategy for building robust models on multiple data sets derived from samples representing real scenarios, for example, a model trained on a combination of real and spike-in mutations had the highest average performance. CONCLUSIONS The strategy identified in our study achieved high robustness across multiple sequencing technologies for fresh and FFPE DNA input, varying tumor/normal purities, and different coverages, with significant superiority over conventional detection approaches in general, as well as in challenging situations such as low coverage, low variant allele frequency, DNA damage, and difficult genomic regions.
Collapse
Affiliation(s)
| | - Li Tai Fang
- Roche Sequencing Solutions, Santa Clara, CA, 95050, USA
| | - Konstantinos Karagiannis
- The Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD, 20993, USA
| | - Malcolm Moos
- The Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD, 20993, USA
| | - Sean Smith
- The Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD, 20993, USA
| | - Luis Santana-Quintero
- The Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD, 20993, USA
| | - Chunlin Xiao
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Michael Colgan
- Office of Oncological Diseases, Office of New Drug, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD, 20993, USA
| | - Huixiao Hong
- Bioinformatics branch, Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA
| | | | - Wenming Xiao
- Office of Oncological Diseases, Office of New Drug, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD, 20993, USA.
| |
Collapse
|
49
|
Sasaki T, Uda T, Kuki I, Kunihiro N, Okazaki S, Niida Y, Goto T. TSC2 somatic mosaic mutation, including extra-tumor tissue, may be the developmental cause of solitary subependymal giant cell astrocytoma. Childs Nerv Syst 2022; 38:77-83. [PMID: 34741623 DOI: 10.1007/s00381-021-05399-y] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/16/2021] [Indexed: 12/01/2022]
Abstract
PURPOSE Subependymal giant cell astrocytomas (SEGAs) are tumors that usually arise in the wall of one or the other lateral ventricle near a foramen of Monro, most often on a background of tuberous sclerosis complex (TSC). TSC has a variety of clinical manifestations caused by germline mutations of the TSC complex subunit 1 or 2 (TSC1, TSC2) genes. SEGAs without clinical manifestations of TSC are termed solitary SEGAs, which are hypothesized to be caused by tumor-only TSC1/2 mutations, or "forme fruste" of TSC with somatic mosaic mutations. However, it is difficult to distinguish between the two. Here, we report three patients with genetically investigated solitary SEGAs and review this rare manifestation. METHODS SEGA was completely removed in two patients and partially removed in one. Genetic analyses were performed on the tumor tissue and on peripheral blood via DNA microarray, reverse-transcriptase polymerase chain reaction, and next-generation sequencing with ultra-deep sequencing of mutation points. RESULTS All three patients had tumors with TSC2 somatic mutations and loss of heterozygosity (LOH). In one patient, the same TSC2 mutation was also detected in 1% of leukocytes in his blood. The tumors did not recur, and clinical manifestations of TSC did not develop during the 4-year follow-up. CONCLUSIONS The genetic cause of solitary SEGAs may be a TSC2 mutation with LOH. In patients with solitary SEGA, mosaic mutations may present in other organs, and TSC may clinically manifest later in life; therefore, patients should be followed up for prolonged periods.
Collapse
Affiliation(s)
- Tsuyoshi Sasaki
- Department of Neurosurgery, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Takehiro Uda
- Department of Neurosurgery, Osaka City University Graduate School of Medicine, Osaka, Japan.
| | - Ichiro Kuki
- Department of Pediatric Neurology, Osaka City General Hospital, Osaka, Japan
| | - Noritsugu Kunihiro
- Department of Pediatric Neurosurgery, Osaka City General Hospital, Osaka, Japan
| | - Shin Okazaki
- Department of Pediatric Neurology, Osaka City General Hospital, Osaka, Japan
| | - Yo Niida
- Center for Clinical Genomics, Kanazawa Medical University Hospital, Kanazawa, Japan
| | - Takeo Goto
- Department of Neurosurgery, Osaka City University Graduate School of Medicine, Osaka, Japan
| |
Collapse
|
50
|
Xu Y, Huang Z, Yu X, Chen K, Fan Y. Integrated genomic and DNA methylation analysis of patients with advanced non-small cell lung cancer with brain metastases. Mol Brain 2021; 14:176. [PMID: 34952628 PMCID: PMC8710019 DOI: 10.1186/s13041-021-00886-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 12/12/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Brain metastasis is a common and lethal complication of non-small cell lung cancer (NSCLC). It is mostly diagnosed only after symptoms develop, at which point very few treatment options are available. Therefore, patients who have an increased risk of developing brain metastasis need to be identified early. Our study aimed to identify genomic and epigenomic biomarkers for predicting brain metastasis risk in NSCLC patients. METHODS Paired primary lung tumor tissues and either brain metastatic tissues or cerebrospinal fluid (CSF) samples were collected from 29 patients with treatment-naïve advanced NSCLC with central nervous system (CNS) metastases. A control group comprising 31 patients with advanced NSCLC who died without ever developing CNS metastasis was also included. Somatic mutations and DNA methylation levels were examined through capture-based targeted sequencing with a 520-gene panel and targeted bisulfite sequencing with an 80,672 CpG panel. RESULTS Compared to primary lung lesions, brain metastatic tissues harbored numerous unique copy number variations. The tumor mutational burden was comparable between brain metastatic tissue (P = 0.168)/CSF (P = 0.445) and their paired primary lung tumor samples. Kelch-like ECH-associated protein (KEAP1) mutations were detected in primary lung tumor and brain metastatic tissue samples of patients with brain metastasis. KEAP1 mutation rate was significantly higher in patients with brain metastasis than those without (P = 0.031). DNA methylation analysis revealed 15 differentially methylated blocks between primary lung tumors of patients with and without CNS metastasis. A brain metastasis risk prediction model based on these 15 differentially methylated blocks had an area under the curve of 0.94, with 87.1% sensitivity and 82.8% specificity. CONCLUSIONS Our analyses revealed 15 differentially methylated blocks in primary lung tumor tissues, which can differentiate patients with and without CNS metastasis. These differentially methylated blocks may serve as predictive biomarkers for the risk of developing CNS metastasis in NSCLC. Additional larger studies are needed to validate the predictive value of these markers.
Collapse
Affiliation(s)
- Yanjun Xu
- Department of Medical Thoracic Oncology, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, No. 1 East Banshan Road, Gongshu District, Hangzhou, 310022, China
| | - Zhiyu Huang
- Department of Medical Thoracic Oncology, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, No. 1 East Banshan Road, Gongshu District, Hangzhou, 310022, China
| | - Xiaoqing Yu
- Department of Medical Thoracic Oncology, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, No. 1 East Banshan Road, Gongshu District, Hangzhou, 310022, China
| | - Kaiyan Chen
- Department of Medical Thoracic Oncology, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, No. 1 East Banshan Road, Gongshu District, Hangzhou, 310022, China
| | - Yun Fan
- Department of Medical Thoracic Oncology, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, No. 1 East Banshan Road, Gongshu District, Hangzhou, 310022, China.
| |
Collapse
|