251
|
Paziewska A, Polkowski M, Goryca K, Karczmarski J, Wiechowska-Kozlowska A, Dabrowska M, Mikula M, Ostrowski J. Mutational Mosaics of Cell-Free DNA from Pancreatic Cyst Fluids. Dig Dis Sci 2020; 65:2294-2301. [PMID: 31925676 DOI: 10.1007/s10620-019-06043-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 12/31/2019] [Indexed: 12/29/2022]
Abstract
BACKGROUND Pancreatic cyst fluids (PCFs) enriched in tumor-derived DNA are a potential source of new biomarkers. The study aimed to analyze germinal variants and mutational profiles of cell-free (cf)DNA shed into the cavity of pancreatic cysts. METHODS The study cohort consisted of 71 patients who underwent endoscopic ultrasound fine-needle aspiration of PCF. Five malignant cysts, 19 intraductal papillary mucinous neoplasms (IPMNs), 11 mucinous cystic neoplasms (MCNs), eight serous cystic neoplasms (SCNs), and 28 pseudocysts were identified. The sequencing of 409 genes included in Comprehensive Cancer Panel was performed using Ion Proton System. The mutation rate of the KRAS and GNAS canonical loci was additionally determined using digital PCR. RESULTS The number of mutations detected with NGS varied from 0 to 22 per gene, and genes with the most mutations were: TP53, KRAS, PIK3CA, GNAS, ADGRA2, and APC. The frequencies of the majority of mutations did not differ between non-malignant cystic neoplasms and pseudocysts. NGS detected KRAS mutations in malignant cysts (60%), IPMNs (32%), MCNs (64%), SCNs (13%), and pseudocysts (14%), with GNAS mutations in 20%, 26%, 27%, 13%, and 21% of samples, respectively. Digital PCR-based testing increased KRAS (68%) and GNAS (52%) mutations detection level in IPMNs, but not other cyst types. CONCLUSIONS We demonstrate relatively high rates of somatic mutations of cancer-related genes, including KRAS and GNAS, in cfDNA isolated from PCFs irrespectively of the pancreatic cyst type. Further studies on molecular mechanisms of pancreatic cysts malignant transformation in relation to their mutational profiles are required.
Collapse
Affiliation(s)
- Agnieszka Paziewska
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Roentgena 5, 02-781, Warsaw, Poland.,Department of Genetics, Maria Sklodowska-Curie Institute-Cancer Center, Roentgena 5, 02-781, Warsaw, Poland
| | - Marcin Polkowski
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Roentgena 5, 02-781, Warsaw, Poland
| | - Krzysztof Goryca
- Department of Genetics, Maria Sklodowska-Curie Institute-Cancer Center, Roentgena 5, 02-781, Warsaw, Poland.,Next Generation Sequencing Core Facility, Centre of New Technologies, University of Warsaw, 02-097, Warsaw, Poland
| | - Jakub Karczmarski
- Department of Genetics, Maria Sklodowska-Curie Institute-Cancer Center, Roentgena 5, 02-781, Warsaw, Poland
| | | | - Michalina Dabrowska
- Department of Genetics, Maria Sklodowska-Curie Institute-Cancer Center, Roentgena 5, 02-781, Warsaw, Poland
| | - Michal Mikula
- Department of Genetics, Maria Sklodowska-Curie Institute-Cancer Center, Roentgena 5, 02-781, Warsaw, Poland
| | - Jerzy Ostrowski
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Roentgena 5, 02-781, Warsaw, Poland. .,Department of Genetics, Maria Sklodowska-Curie Institute-Cancer Center, Roentgena 5, 02-781, Warsaw, Poland.
| |
Collapse
|
252
|
Kang T, Yau C, Wong CK, Sanborn JZ, Newton Y, Vaske C, Benz SC, Krings G, Camarda R, Henry JE, Stuart J, Powell M, Benz CC. A risk-associated Active transcriptome phenotype expressed by histologically normal human breast tissue and linked to a pro-tumorigenic adipocyte population. Breast Cancer Res 2020; 22:81. [PMID: 32736587 PMCID: PMC7395362 DOI: 10.1186/s13058-020-01322-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 07/23/2020] [Indexed: 01/04/2023] Open
Abstract
Background Previous studies have identified and validated a risk-associated Active transcriptome phenotype commonly expressed in the cancer-adjacent and histologically normal epithelium, stroma, and adipose containing peritumor microenvironment of clinically established invasive breast cancers, conferring a 2.5- to 3-fold later risk of dying from recurrent breast cancer. Expression of this Active transcriptome phenotype has not yet been evaluated in normal breast tissue samples unassociated with any benign or malignant lesions; however, it has been associated with increased peritumor adipocyte composition. Methods Detailed histologic and transcriptomic (RNAseq) analyses were performed on normal breast biopsy samples from 151 healthy, parous, non-obese (mean BMI = 29.60 ± 7.92) women, ages 27–66 who donated core breast biopsy samples to the Komen Tissue Bank, and whose average breast cancer risk estimate (Gail score) at the time of biopsy (1.27 ± 1.34) would not qualify them for endocrine prevention therapy. Results Full genome RNA sequencing (RNAseq) identified 52% (78/151) of these normal breast samples as expressing the Active breast phenotype. While Active signature genes were found to be most variably expressed in mammary adipocytes, donors with the Active phenotype had no difference in BMI but significantly higher Gail scores (1.46 vs. 1.18; p = 0.007). Active breast samples possessed 1.6-fold more (~ 80%) adipocyte nuclei, larger cross-sectional adipocyte areas (p < 0.01), and 0.5-fold fewer stromal and epithelial cell nuclei (p < 1e−6). Infrequent low-level expression of cancer gene hotspot mutations was detected but not enriched in the Active breast samples. Active samples were enriched in gene sets associated with adipogenesis and fat metabolism (FDR q ≤ 10%), higher signature scores for cAMP-dependent lipolysis known to drive breast cancer progression, white adipose tissue browning (Wilcoxon p < 0.01), and genes associated with adipocyte activation (leptin, adiponectin) and remodeling (CAV1, BNIP3), adipokine growth factors (IGF-1, FGF2), and pro-inflammatory fat signaling (IKBKG, CCL13). Conclusions The risk-associated Active transcriptome phenotype first identified in cancer-adjacent breast tissues also occurs commonly in healthy women without breast disease who do not qualify for breast cancer chemoprevention, and independently of breast expressed cancer-associated mutations. The risk-associated Active phenotype appears driven by a pro-tumorigenic adipocyte microenvironment that can predate breast cancer development.
Collapse
Affiliation(s)
- Taekyu Kang
- Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA, 94945, USA
| | - Christina Yau
- Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA, 94945, USA
| | | | | | | | | | | | | | - Roman Camarda
- Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA, 94945, USA
| | - Jill E Henry
- Susan G. Komen Tissue Bank at the Indiana University Simon Cancer Center, Indianapolis, IN, USA
| | - Josh Stuart
- University of California, Genomics Institute, Santa Cruz, CA, USA
| | - Mark Powell
- Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA, 94945, USA
| | - Christopher C Benz
- Buck Institute for Research on Aging, 8001 Redwood Blvd., Novato, CA, 94945, USA.
| |
Collapse
|
253
|
Kadosh E, Snir-Alkalay I, Venkatachalam A, May S, Lasry A, Elyada E, Zinger A, Shaham M, Vaalani G, Mernberger M, Stiewe T, Pikarsky E, Oren M, Ben-Neriah Y. The gut microbiome switches mutant p53 from tumour-suppressive to oncogenic. Nature 2020; 586:133-138. [PMID: 32728212 PMCID: PMC7116712 DOI: 10.1038/s41586-020-2541-0] [Citation(s) in RCA: 223] [Impact Index Per Article: 55.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 05/01/2020] [Indexed: 12/16/2022]
Abstract
Somatic mutations in p53, which inactivate the tumour-suppressor function of p53 and often confer oncogenic gain-of-function properties, are very common in cancer1,2. Here we studied the effects of hotspot gain-of-function mutations in Trp53 (the gene that encodes p53 in mice) in mouse models of WNT-driven intestinal cancer caused by Csnk1a1 deletion3,4 or ApcMin mutation5. Cancer in these models is known to be facilitated by loss of p533,6. We found that mutant versions of p53 had contrasting effects in different segments of the gut: in the distal gut, mutant p53 had the expected oncogenic effect; however, in the proximal gut and in tumour organoids it had a pronounced tumour-suppressive effect. In the tumour-suppressive mode, mutant p53 eliminated dysplasia and tumorigenesis in Csnk1a1-deficient and ApcMin/+ mice, and promoted normal growth and differentiation of tumour organoids derived from these mice. In these settings, mutant p53 was more effective than wild-type p53 at inhibiting tumour formation. Mechanistically, the tumour-suppressive effects of mutant p53 were driven by disruption of the WNT pathway, through preventing the binding of TCF4 to chromatin. Notably, this tumour-suppressive effect was completely abolished by the gut microbiome. Moreover, a single metabolite derived from the gut microbiota–gallic acid–could reproduce the entire effect of the microbiome. Supplementing gut-sterilized p53-mutant mice and p53-mutant organoids with gallic acid reinstated the TCF4–chromatin interaction and the hyperactivation of WNT, thus conferring a malignant phenotype to the organoids and throughout the gut. Our study demonstrates the substantial plasticity of a cancer mutation and highlights the role of the microenvironment in determining its functional outcome.
Collapse
Affiliation(s)
- Eliran Kadosh
- The Lautenberg Center for Immunology and Cancer Research, Institute of Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Irit Snir-Alkalay
- The Lautenberg Center for Immunology and Cancer Research, Institute of Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Avanthika Venkatachalam
- The Lautenberg Center for Immunology and Cancer Research, Institute of Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Shahaf May
- The Lautenberg Center for Immunology and Cancer Research, Institute of Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Audrey Lasry
- The Lautenberg Center for Immunology and Cancer Research, Institute of Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel.,Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Ela Elyada
- The Lautenberg Center for Immunology and Cancer Research, Institute of Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel.,Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Adar Zinger
- The Lautenberg Center for Immunology and Cancer Research, Institute of Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Maya Shaham
- The Lautenberg Center for Immunology and Cancer Research, Institute of Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Gitit Vaalani
- The Lautenberg Center for Immunology and Cancer Research, Institute of Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Marco Mernberger
- Institute of Molecular Oncology, Genomics Core Facility, Philipps University Marburg, Marburg, Germany
| | - Thorsten Stiewe
- Institute of Molecular Oncology, Genomics Core Facility, Philipps University Marburg, Marburg, Germany
| | - Eli Pikarsky
- The Lautenberg Center for Immunology and Cancer Research, Institute of Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Moshe Oren
- Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Yinon Ben-Neriah
- The Lautenberg Center for Immunology and Cancer Research, Institute of Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel.
| |
Collapse
|
254
|
Credendino SC, Neumayer C, Cantone I. Genetics and Epigenetics of Sex Bias: Insights from Human Cancer and Autoimmunity. Trends Genet 2020; 36:650-663. [PMID: 32736810 DOI: 10.1016/j.tig.2020.06.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/23/2020] [Accepted: 06/24/2020] [Indexed: 12/17/2022]
Abstract
High-throughput sequencing and genome-wide association studies have revealed a sex bias in human diseases. The underlying molecular mechanisms remain, however, unknown. Here, we cover recent advances in cancer and autoimmunity focusing on intrinsic genetic and epigenetic differences underlying sex biases in human disease. These studies reveal a central role of genome regulatory mechanisms including genome repair, chromosome folding, and epigenetic regulation in dictating the sex bias. These highlight the importance of considering sex as a variable in both basic science and clinical investigations. Understanding the molecular mechanisms underlying sex bias in human diseases will be instrumental in making a first step forwards into the era of personalized medicine.
Collapse
Affiliation(s)
- Sara Carmela Credendino
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy
| | - Christoph Neumayer
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy
| | - Irene Cantone
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; Institute of Experimental Endocrinology and Oncology 'G. Salvatore', National Research Council (CNR), 80131 Naples, Italy.
| |
Collapse
|
255
|
Limited Practical Utility of Liquid Biopsy in the Treated Patients with Advanced Breast Cancer. Diagnostics (Basel) 2020; 10:diagnostics10080523. [PMID: 32731384 PMCID: PMC7460238 DOI: 10.3390/diagnostics10080523] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 07/24/2020] [Indexed: 12/16/2022] Open
Abstract
Recently, liquid biopsy has emerged as a tool to monitor oncologic disease progression and the effects of treatment. In this study we aimed to determine the clinical utility of liquid biopsy relative to conventional oncological post-treatment surveillance. Plasma cell-free (cf) DNA was collected from six healthy women and 37 patients with breast cancer (18 and 19 with stage III and IV tumors, respectively). CfDNA was assessed using the Oncomine Pan-Cancer Cell-Free Assay. In cfDNA samples from patients with BC, 1112 variants were identified, with only a few recurrent or hotspot mutations within specific regions of cancer genes. Of 65 potentially pathogenic variants detected in tumors, only 19 were also discovered in at least one blood sample. The allele frequencies of detected variants (VAFs) were <1% in cfDNA from all controls and patients with stage III BC, and 24/85 (28.2%) variants had VAFs > 1% in only 8 of 25 (32%) patients with stage IV BC. Copy number variations (CNVs) spanning CDK4, MET, FGFR1, FGFR2, ERBB2, MYC, and CCND3 were found in 1 of 12 (8%) and 8 of 25 (32%) patients with stage III and IV tumors, respectively. In healthy controls and patients without BC progression after treatment, VAFs were <1%, while in patients with metastatic disease and/or more advanced genomic alterations, VAFs > 1% and/or CNV were detected in approximately 30%. Therefore, most patients with stage IV BC could not be distinguished from those with stage III disease following therapy, based on liquid biopsy results.
Collapse
|
256
|
Oh JH, Sung CO. Comprehensive characteristics of somatic mutations in the normal tissues of patients with cancer and existence of somatic mutant clones linked to cancer development. J Med Genet 2020; 58:433-441. [PMID: 32719100 DOI: 10.1136/jmedgenet-2020-106905] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 06/02/2020] [Accepted: 06/04/2020] [Indexed: 12/30/2022]
Abstract
BACKGROUND Somatic mutations are a major driver of cancer development and many have now been identified in various cancer types, but the comprehensive somatic mutation status of the normal tissues matched to tumours has not been revealed. METHOD We analysed the somatic mutations of whole exome sequencing data in 392 patient tumour and normal tissue pairs based on the corresponding blood samples across 10 tumour types. RESULTS Many of the mutations involved in oncogenic pathways such as PI3K, NOTCH and TP53, were identified in the normal tissues. The ageing-related mutational signature was the most prominent contributing signature found and the mutations in the normal tissues were frequently in genes involved in late replication time (p<0.0001). Variants were rarely overlapping across tissue types but shared variants between normal and matched tumour tissue were present. These shared variants were frequently pathogenic when compared with non-shared variants (p=0.001) and showed a higher variant-allele-fraction (p<0.0001). Normal tissue-specific mutated genes were frequently non-cancer-associated (p=0.009). PIK3CA mutations were identified in 6 normal tissues and were harboured by all of the matched cancer tissues. Multiple types of PIK3CA mutations were found in normal breast and matched cancer tissues. The PIK3CA mutations exclusively present in normal tissue may indicate clonal expansions unrelated to the tumour. In addition, PIK3CA mutation was appeared that they arose before the occurrence of the allelic imbalance. CONCLUSION Our current results suggest that somatic mutant clones exist in normal tissues and that their clonal expansion could be linked to cancer development.
Collapse
Affiliation(s)
- Ji-Hye Oh
- Center for Cancer Genome Discovery, Asan Institute for Life Science, Asan Medical Center, Songpa-gu, Seoul, The Republic of Korea.,Department of Medical Science, Asan Medical Institute of Convergence Science and Technology, University of Ulsan College of Medicine, Songpa-gu, Seoul, The Republic of Korea
| | - Chang Ohk Sung
- Center for Cancer Genome Discovery, Asan Institute for Life Science, Asan Medical Center, Songpa-gu, Seoul, The Republic of Korea .,Department of Medical Science, Asan Medical Institute of Convergence Science and Technology, University of Ulsan College of Medicine, Songpa-gu, Seoul, The Republic of Korea.,Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Songpa-gu, Seoul, The Republic of Korea
| |
Collapse
|
257
|
Paracchini L, Pesenti C, Delle Marchette M, Beltrame L, Bianchi T, Grassi T, Buda A, Landoni F, Ceppi L, Bosetti C, Paderno M, Adorni M, Vicini D, Perego P, Leone BE, D’Incalci M, Marchini S, Fruscio R. Detection of TP53 Clonal Variants in Papanicolaou Test Samples Collected up to 6 Years Prior to High-Grade Serous Epithelial Ovarian Cancer Diagnosis. JAMA Netw Open 2020; 3:e207566. [PMID: 32609349 PMCID: PMC7330718 DOI: 10.1001/jamanetworkopen.2020.7566] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
IMPORTANCE The low 5-year survival rate of women with high-grade serous epithelial ovarian cancer (HGS-EOC) is related to its late diagnosis; thus, improvement in diagnosis constitutes a crucial step to increase the curability of this disease. OBJECTIVE To determine whether the presence of the clonal pathogenic TP53 variant detected in matched primary tumor biopsies can be identified in DNA purified from Papanicolaou test samples collected from women with HGS-EOC years before the diagnosis. DESIGN, SETTING, AND PARTICIPANTS This cohort study was conducted among a single-center cohort of women with histologically confirmed diagnosis of HGS-EOC recruited at San Gerardo Hospital, Monza, Italy, from October 15, 2015, to January 4, 2019. Serial dilutions of DNA derived from tumor samples and DNA extracted from healthy women's Papanicolaou test samples were analyzed to define the sensitivity and specificity of droplet digital polymerase chain reaction assays designed to detect the TP53 variants identified in tumors. All available brush-based Papanicolaou test slides performed up to 6 years before diagnosis were investigated at the Mario Negri Institute, Milano, Italy. Data were analyzed from October 2018 to December 2019. MAIN OUTCOMES AND MEASURES The presence of tumor pathogenic TP53 variants was assessed by the droplet digital polymerase chain reaction approach in DNA purified from Papanicolaou test samples obtained from the same patients before diagnosis during cervical cancer screenings. RESULTS Among 17 included patients (median [interquartile range] age at diagnosis, 60 [53-69] years), Papanicolaou tests withdrawn before diagnosis presented tumor-matched TP53 variants in 11 patients (64%). In 2 patients for whom longitudinal Papanicolaou tests were available, including 1 patient with Papanicolaou tests from 25 and 49 months before diagnosis and 1 patient with Papanicolaou tests from 27 and 68 months before diagnosis, the TP53 clonal variant was detected at all time points. CONCLUSIONS AND RELEVANCE These findings suggest that noninvasive early molecular diagnosis of HGS-EOC is potentially achievable through detection of TP53 clonal variants in the DNA purified from Papanicolaou tests performed during cervical cancer screening.
Collapse
Affiliation(s)
- Lara Paracchini
- Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Chiara Pesenti
- Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Martina Delle Marchette
- Department of Obstetrics and Gynecology, Università degli Studi Milano-Bicocca, San Gerardo Hospital, Monza, Italy
| | - Luca Beltrame
- Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Tommaso Bianchi
- Department of Obstetrics and Gynecology, Università degli Studi Milano-Bicocca, San Gerardo Hospital, Monza, Italy
| | - Tommaso Grassi
- Department of Obstetrics and Gynecology, Università degli Studi Milano-Bicocca, San Gerardo Hospital, Monza, Italy
| | - Alessandro Buda
- Department of Obstetrics and Gynecology, Università degli Studi Milano-Bicocca, San Gerardo Hospital, Monza, Italy
| | - Fabio Landoni
- Department of Obstetrics and Gynecology, Università degli Studi Milano-Bicocca, San Gerardo Hospital, Monza, Italy
| | - Lorenzo Ceppi
- Department of Obstetrics and Gynecology, Azienda Socio Sanitaria Territoriale -Monza, Desio Hospital, Desio, Italy
| | - Cristina Bosetti
- Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Mariachiara Paderno
- Department of Obstetrics and Gynecology, Università degli Studi Milano-Bicocca, San Gerardo Hospital, Monza, Italy
| | - Marco Adorni
- Department of Obstetrics and Gynecology, Università degli Studi Milano-Bicocca, San Gerardo Hospital, Monza, Italy
| | - Debora Vicini
- Department of Obstetrics and Gynecology, Università degli Studi Milano-Bicocca, San Gerardo Hospital, Monza, Italy
| | - Patrizia Perego
- Department of Pathology, Università degli Studi Milano-Bicocca, San Gerardo Hospital, Monza, Italy
| | - Biagio Eugenio Leone
- Department of Pathology, Università degli Studi Milano-Bicocca, San Gerardo Hospital, Monza, Italy
| | - Maurizio D’Incalci
- Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Sergio Marchini
- Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Robert Fruscio
- Department of Obstetrics and Gynecology, Università degli Studi Milano-Bicocca, San Gerardo Hospital, Monza, Italy
| |
Collapse
|
258
|
Kazianka L, Staber PB. The Bone's Role in Myeloid Neoplasia. Int J Mol Sci 2020; 21:E4712. [PMID: 32630305 PMCID: PMC7369750 DOI: 10.3390/ijms21134712] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/16/2020] [Accepted: 06/26/2020] [Indexed: 02/07/2023] Open
Abstract
The interaction of hematopoietic stem and progenitor cells with their direct neighboring cells in the bone marrow (the so called hematopoietic niche) evolves as a key principle for understanding physiological and malignant hematopoiesis. Significant progress in this matter has recently been achieved making use of emerging high-throughput techniques that allow characterization of the bone marrow microenvironment at single cell resolution. This review aims to discuss these single cell findings in the light of other conventional niche studies that together define the current notion of the niche's implication in i) normal hematopoiesis, ii) myeloid neoplasms and iii) disease-driving pathways that can be exploited to establish novel therapeutic strategies in the future.
Collapse
Affiliation(s)
| | - Philipp B Staber
- Division of Hematology and Hemostaseology, Department of Medicine I, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna, Austria;
| |
Collapse
|
259
|
Castel P, Rauen KA, McCormick F. The duality of human oncoproteins: drivers of cancer and congenital disorders. Nat Rev Cancer 2020; 20:383-397. [PMID: 32341551 PMCID: PMC7787056 DOI: 10.1038/s41568-020-0256-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/20/2020] [Indexed: 01/29/2023]
Abstract
Human oncoproteins promote transformation of cells into tumours by dysregulating the signalling pathways that are involved in cell growth, proliferation and death. Although oncoproteins were discovered many years ago and have been widely studied in the context of cancer, the recent use of high-throughput sequencing techniques has led to the identification of cancer-associated mutations in other conditions, including many congenital disorders. These syndromes offer an opportunity to study oncoprotein signalling and its biology in the absence of additional driver or passenger mutations, as a result of their monogenic nature. Moreover, their expression in multiple tissue lineages provides insight into the biology of the proto-oncoprotein at the physiological level, in both transformed and unaffected tissues. Given the recent paradigm shift in regard to how oncoproteins promote transformation, we review the fundamentals of genetics, signalling and pathogenesis underlying oncoprotein duality.
Collapse
Affiliation(s)
- Pau Castel
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
| | - Katherine A Rauen
- MIND Institute, Department of Pediatrics, University of California, Davis, Sacramento, CA, USA
| | - Frank McCormick
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| |
Collapse
|
260
|
Zviran A, Schulman RC, Shah M, Hill STK, Deochand S, Khamnei CC, Maloney D, Patel K, Liao W, Widman AJ, Wong P, Callahan MK, Ha G, Reed S, Rotem D, Frederick D, Sharova T, Miao B, Kim T, Gydush G, Rhoades J, Huang KY, Omans ND, Bolan PO, Lipsky AH, Ang C, Malbari M, Spinelli CF, Kazancioglu S, Runnels AM, Fennessey S, Stolte C, Gaiti F, Inghirami GG, Adalsteinsson V, Houck-Loomis B, Ishii J, Wolchok JD, Boland G, Robine N, Altorki NK, Landau DA. Genome-wide cell-free DNA mutational integration enables ultra-sensitive cancer monitoring. Nat Med 2020; 26:1114-1124. [PMID: 32483360 PMCID: PMC8108131 DOI: 10.1038/s41591-020-0915-3] [Citation(s) in RCA: 196] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 04/29/2020] [Indexed: 12/21/2022]
Abstract
In many areas of oncology, we lack sensitive tools to track low-burden disease. Although cell-free DNA (cfDNA) shows promise in detecting cancer mutations, we found that the combination of low tumor fraction (TF) and limited number of DNA fragments restricts low-disease-burden monitoring through the prevailing deep targeted sequencing paradigm. We reasoned that breadth may supplant depth of sequencing to overcome the barrier of cfDNA abundance. Whole-genome sequencing (WGS) of cfDNA allowed ultra-sensitive detection, capitalizing on the cumulative signal of thousands of somatic mutations observed in solid malignancies, with TF detection sensitivity as low as 10-5. The WGS approach enabled dynamic tumor burden tracking and postoperative residual disease detection, associated with adverse outcome. Thus, we present an orthogonal framework for cfDNA cancer monitoring via genome-wide mutational integration, enabling ultra-sensitive detection, overcoming the limitation of cfDNA abundance and empowering treatment optimization in low-disease-burden oncology care.
Collapse
Affiliation(s)
- Asaf Zviran
- New York Genome Center, New York, NY, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Rafael C Schulman
- New York Genome Center, New York, NY, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | | | - Steven T K Hill
- New York Genome Center, New York, NY, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Sunil Deochand
- New York Genome Center, New York, NY, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Cole C Khamnei
- New York Genome Center, New York, NY, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | | | - Kristofer Patel
- New York Genome Center, New York, NY, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Will Liao
- New York Genome Center, New York, NY, USA
| | - Adam J Widman
- New York Genome Center, New York, NY, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Phillip Wong
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Margaret K Callahan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gavin Ha
- Division of Public Health Services, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Sarah Reed
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Denisse Rotem
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Dennie Frederick
- Division of Surgical Oncology, Massachussetts General Hospital, Boston, MA, USA
| | - Tatyana Sharova
- Division of Surgical Oncology, Massachussetts General Hospital, Boston, MA, USA
| | - Benchun Miao
- Division of Surgical Oncology, Massachussetts General Hospital, Boston, MA, USA
| | - Tommy Kim
- Division of Surgical Oncology, Massachussetts General Hospital, Boston, MA, USA
| | - Greg Gydush
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Kevin Y Huang
- New York Genome Center, New York, NY, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Nathaniel D Omans
- New York Genome Center, New York, NY, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Patrick O Bolan
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Andrew H Lipsky
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Chelston Ang
- New York Genome Center, New York, NY, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Murtaza Malbari
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | | | | | | | | | | | - Federico Gaiti
- New York Genome Center, New York, NY, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | | | | | | | | | - Jedd D Wolchok
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Genevieve Boland
- Division of Surgical Oncology, Massachussetts General Hospital, Boston, MA, USA
| | | | | | - Dan A Landau
- New York Genome Center, New York, NY, USA.
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
| |
Collapse
|
261
|
Affiliation(s)
- Eric Solary
- INSERM U1287 Gustave Roussy Cancer Center Villejuif France
- Faculté de Médecine Université Paris‐Saclay Le Kremlin‐Bicêtre France
| | - Lucie Laplane
- INSERM U1287 Gustave Roussy Cancer Center Villejuif France
- CNRS U8590 Institut d'Histoire et Philosophie des Sciences et des Techniques Université Paris I Panthéon‐Sorbonne Paris France
| |
Collapse
|
262
|
Yang Q, Shen Y, Shao C, Liu Y, Xu H, Zhou Y, Liu Z, Sun K, Tang Q, Xie J. Genetic analysis of tri-allelic patterns at the CODIS STR loci. Mol Genet Genomics 2020; 295:1263-1268. [DOI: 10.1007/s00438-020-01701-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 06/09/2020] [Indexed: 11/28/2022]
|
263
|
ILK silencing inhibits migration and invasion of more invasive glioblastoma cells by downregulating ROCK1 and Fascin-1. Mol Cell Biochem 2020; 471:143-153. [PMID: 32506247 DOI: 10.1007/s11010-020-03774-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 05/31/2020] [Indexed: 12/23/2022]
Abstract
Glioblastoma multiforme (GBM) is the most aggressive type of brain tumor and it is associated with poor survival. Integrin-linked kinase (ILK) is a serine/threonine protein pseudo-kinase that binds to the cytoplasmic domains of β1 and β3 integrins and has been previously shown to promote invasion and metastasis in many cancer types, including GBM. However, little is known regarding the exact molecular mechanism implicating ILK in GBM aggressiveness. In this study, we used two brain cell lines, the non-invasive neuroglioma H4 cells, and the highly invasive glioblastoma A172 cells, which express ILK in much higher levels than H4. We studied the effect of ILK silencing on the metastatic behavior of glioblastoma cells in vitro and elucidate the underlying molecular mechanism. We showed that siRNA-mediated silencing of ILK inhibits cell migration and invasion of the highly invasive A172 cells while it does not affect the migratory and invasive capacity of H4 cells. These data were also supported by respective changes in the expression of Rho-associated kinase 1 (ROCK1), fascin actin-bundling protein 1 (FSCN1), and matrix metalloproteinase 13 (MMP13), which are known to regulate cell migration and invasion. Our findings were further corroborated by analyzing the Cancer Genome Atlas Glioblastoma Multiforme (TCGA-GBM) dataset. We conclude that ILK promotes glioblastoma cell invasion through activation of ROCK1 and FSCN1 in vitro, providing a more exact molecular mechanism for its action.
Collapse
|
264
|
Muyas F, Zapata L, Guigó R, Ossowski S. The rate and spectrum of mosaic mutations during embryogenesis revealed by RNA sequencing of 49 tissues. Genome Med 2020; 12:49. [PMID: 32460841 PMCID: PMC7254727 DOI: 10.1186/s13073-020-00746-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 05/08/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Mosaic mutations acquired during early embryogenesis can lead to severe early-onset genetic disorders and cancer predisposition, but are often undetectable in blood samples. The rate and mutational spectrum of embryonic mosaic mutations (EMMs) have only been studied in few tissues, and their contribution to genetic disorders is unknown. Therefore, we investigated how frequent mosaic mutations occur during embryogenesis across all germ layers and tissues. METHODS Mosaic mutation detection in 49 normal tissues from 570 individuals (Genotype-Tissue Expression (GTEx) cohort) was performed using a newly developed multi-tissue, multi-individual variant calling approach for RNA-seq data. Our method allows for reliable identification of EMMs and the developmental stage during which they appeared. RESULTS The analysis of EMMs in 570 individuals revealed that newborns on average harbor 0.5-1 EMMs in the exome affecting multiple organs (1.3230 × 10-8 per nucleotide per individual), a similar frequency as reported for germline de novo mutations. Our multi-tissue, multi-individual study design allowed us to distinguish mosaic mutations acquired during different stages of embryogenesis and adult life, as well as to provide insights into the rate and spectrum of mosaic mutations. We observed that EMMs are dominated by a mutational signature associated with spontaneous deamination of methylated cytosines and the number of cell divisions. After birth, cells continue to accumulate somatic mutations, which can lead to the development of cancer. Investigation of the mutational spectrum of the gastrointestinal tract revealed a mutational pattern associated with the food-borne carcinogen aflatoxin, a signature that has so far only been reported in liver cancer. CONCLUSIONS In summary, our multi-tissue, multi-individual study reveals a surprisingly high number of embryonic mosaic mutations in coding regions, implying novel hypotheses and diagnostic procedures for investigating genetic causes of disease and cancer predisposition.
Collapse
Affiliation(s)
- Francesc Muyas
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
| | - Luis Zapata
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Roderic Guigó
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Stephan Ossowski
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
| |
Collapse
|
265
|
The Hippo Pathway as a Driver of Select Human Cancers. Trends Cancer 2020; 6:781-796. [PMID: 32446746 DOI: 10.1016/j.trecan.2020.04.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/20/2020] [Accepted: 04/20/2020] [Indexed: 12/11/2022]
Abstract
The Hippo pathway regulates myriad biological processes in diverse species and is a key cancer signaling network in humans. Although Hippo has been linked to multiple aspects of cancer, its role in this disease is incompletely understood. Large-scale pan-cancer analyses of core Hippo pathway genes reveal that the pathway is mutated at a high frequency only in select human cancers, including malignant mesothelioma and meningioma. Hippo pathway deregulation is also enriched in squamous epithelial cancers. We discuss cancer-related functions of the Hippo pathway and potential explanations for the cancer-restricted mutation profile of core Hippo pathway genes. Greater understanding of Hippo pathway deregulation in cancers will be essential to guide the imminent use of Hippo-targeted therapies.
Collapse
|
266
|
Abstract
As people age, their tissues accumulate an increasing number of somatic mutations. Although most of these mutations are of little or no functional consequence, a mutation may arise that confers a fitness advantage on a cell. When this process happens in the hematopoietic system, a substantial proportion of circulating blood cells may derive from a single mutated stem cell. This outgrowth, called "clonal hematopoiesis," is highly prevalent in the elderly population. Here we discuss recent advances in our knowledge of clonal hematopoiesis, its relationship to malignancies, its link to nonmalignant diseases of aging, and its potential impact on immune function. Clonal hematopoiesis provides a glimpse into the process of mutation and selection that likely occurs in all somatic tissues.
Collapse
Affiliation(s)
- Siddhartha Jaiswal
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Benjamin L Ebert
- Department of Medical Oncology, Howard Hughes Medical Institute, Boston, MA. .,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| |
Collapse
|
267
|
Marderstein AR, Uppal M, Verma A, Bhinder B, Tayyebi Z, Mezey J, Clark AG, Elemento O. Demographic and genetic factors influence the abundance of infiltrating immune cells in human tissues. Nat Commun 2020; 11:2213. [PMID: 32371927 PMCID: PMC7200670 DOI: 10.1038/s41467-020-16097-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 04/13/2020] [Indexed: 12/12/2022] Open
Abstract
Despite infiltrating immune cells having an essential function in human disease and patients' responses to treatments, mechanisms influencing variability in infiltration patterns remain unclear. Here, using bulk RNA-seq data from 46 tissues in the Genotype-Tissue Expression project, we apply cell-type deconvolution algorithms to evaluate the immune landscape across the healthy human body. We discover that 49 of 189 infiltration-related phenotypes are associated with either age or sex (FDR < 0.1). Genetic analyses further show that 31 infiltration-related phenotypes have genome-wide significant associations (iQTLs) (P < 5.0 × 10-8), with a significant enrichment of same-tissue expression quantitative trait loci in suggested iQTLs (P < 10-5). Furthermore, we find an association between helper T cell content in thyroid tissue and a COMMD3/DNAJC1 regulatory variant (P = 7.5 × 10-10), which is associated with thyroiditis in other cohorts. Together, our results identify key factors influencing inter-individual variability of immune infiltration, to provide insights on potential therapeutic targets.
Collapse
Affiliation(s)
- Andrew R Marderstein
- Tri-Institutional Program in Computational Biology & Medicine, Weill Cornell Medicine, New York, NY, USA
- Institute of Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | - Manik Uppal
- Institute of Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Akanksha Verma
- Tri-Institutional Program in Computational Biology & Medicine, Weill Cornell Medicine, New York, NY, USA
- Institute of Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Bhavneet Bhinder
- Institute of Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Zakieh Tayyebi
- Tri-Institutional Program in Computational Biology & Medicine, Weill Cornell Medicine, New York, NY, USA
- Institute of Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Jason Mezey
- Tri-Institutional Program in Computational Biology & Medicine, Weill Cornell Medicine, New York, NY, USA
- Institute of Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | - Andrew G Clark
- Tri-Institutional Program in Computational Biology & Medicine, Weill Cornell Medicine, New York, NY, USA.
- Department of Computational Biology, Cornell University, Ithaca, NY, USA.
| | - Olivier Elemento
- Tri-Institutional Program in Computational Biology & Medicine, Weill Cornell Medicine, New York, NY, USA.
- Institute of Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA.
| |
Collapse
|
268
|
Rezaei S, Donaldson B, Villagomez DAF, Revay T, Mary N, Grossi DA, King WA. Routine Karyotyping Reveals Frequent Mosaic Reciprocal Chromosome Translocations in Swine: Prevalence, Pedigree, and Litter Size. Sci Rep 2020; 10:7471. [PMID: 32366875 PMCID: PMC7198520 DOI: 10.1038/s41598-020-64134-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 04/01/2020] [Indexed: 11/09/2022] Open
Abstract
In the routine commercial karyotype analysis on 5,481 boars, we identified 32 carriers of mosaic reciprocal translocations, half of which were carrying a specific recurrent translocation, mos t(7;9). An additional 7 mosaic translocations were identified through lymphocyte karyotype analysis from parents and relatives of mosaic carriers (n = 45), a control group of non-carrier boars (n = 73), and a mitogen assessment study (n = 20), bringing the total number of mosaic carriers to 39 cases. Mosaic translocations in all carriers were recognized to be confined to hematopoietic cells as no translocations were identified in fibroblasts cells of the carriers. In addition, negative impact on reproduction was not observed as the fertility of the carriers and their relatives were comparable to breed averages, and cryptic mosaicism was not detected in the family tree. This paper presents the first study of mosaic reciprocal translocations identified in swine through routine screening practices on reproductively unproven breeding boars while presenting evidence that these type of chromosome abnormalities are not associated with any affected phenotype on the carrier animals. In addition, the detection of recurrent mosaic translocations in this study may emphasize the non-random nature of mosaic rearrangements in swine and the potential role of genomic elements in their formation.
Collapse
Affiliation(s)
- Samira Rezaei
- Department of Biomedical Sciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Brendan Donaldson
- Department of Biomedical Sciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Daniel A F Villagomez
- Departamento de Produccion Animal, Universidad de Guadalajara, Zapopan, 44100, Mexico
| | - Tamas Revay
- Department of Biomedical Sciences, University of Guelph, Guelph, ON, N1G 2W1, Canada.,Alberta Children's Hospital Research Institute (ACHRI), University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Nicolas Mary
- UMR INRA-ENVT 444 Génétique Cellulaire, École Nationale Vétérinaire de Toulouse, 23 Chemin des Capelles - BP 87614, 31076, Toulouse, Cedex 3, France
| | - Daniela A Grossi
- Fast Genetics, 8,4001 Millar Avenue, Saskatoon, SK, S7K 2K6, Canada
| | - W Allan King
- Department of Biomedical Sciences, University of Guelph, Guelph, ON, N1G 2W1, Canada. .,Karyotekk Inc. Box 363 OVC, University of Guelph, Guelph, ON, N1G 2W1, Canada.
| |
Collapse
|
269
|
Melki PN, Korenjak M, Zavadil J. Experimental investigations of carcinogen-induced mutation spectra: Innovation, challenges and future directions. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2020; 853:503195. [PMID: 32522347 DOI: 10.1016/j.mrgentox.2020.503195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 03/30/2020] [Accepted: 04/02/2020] [Indexed: 11/18/2022]
Abstract
Recent years have witnessed an expansion of mutagenesis research focusing on experimentally modeled genome-scale mutational signatures of carcinogens and of endogenous processes. Experimental mutational signatures can explain etiologic links to patterns found in human tumors that may be linked to same exposures, and can serve as biomarkers of exposure history and may even provide insights on causality. A number of innovative exposure models have been employed and reported, based on cells cultured in monolayers or in 3-D, on organoids, induced pluripotent stem cells, non-mammalian organisms, microorganisms and rodent bioassays. Here we discuss some of the latest developments and pros and cons of these experimental systems used in mutational signature analysis. Integrative designs that bring together multiple exposure systems (in vitro, in vivo and in silico pan-cancer data mining) started emerging as powerful tools to identify robust mutational signatures of the tested cancer risk agents. We further propose that devising a new generation of cell-based models is warranted to streamline systematic testing of carcinogen effects on the cell genomes, while seeking to increasingly supplant animal with non-animal systems to address relevant ethical issues and accentuate the 3R principles. We conclude that the knowledge accumulating from the growing body of signature modelling investigations has considerable power to advance cancer etiology studies and to support cancer prevention efforts through streamlined characterization of cancer-causing agents and the recognition of their specific effects.
Collapse
Affiliation(s)
- Pamela N Melki
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, World Health Organization, 69008 Lyon, France
| | - Michael Korenjak
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, World Health Organization, 69008 Lyon, France
| | - Jiri Zavadil
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, World Health Organization, 69008 Lyon, France.
| |
Collapse
|
270
|
Oishi Y, Manabe I. Organ System Crosstalk in Cardiometabolic Disease in the Age of Multimorbidity. Front Cardiovasc Med 2020; 7:64. [PMID: 32411724 PMCID: PMC7198858 DOI: 10.3389/fcvm.2020.00064] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 03/27/2020] [Indexed: 12/11/2022] Open
Abstract
The close association among cardiovascular, metabolic, and kidney diseases suggests a common pathological basis and significant interaction among these diseases. Metabolic syndrome and cardiorenal syndrome are two examples that exemplify the interlinked development of disease or dysfunction in two or more organs. Recent studies have been sorting out the mechanisms responsible for the crosstalk among the organs comprising the cardiovascular, metabolic, and renal systems, including heart-kidney and adipose-liver signaling, among many others. However, it is also becoming clear that this crosstalk is not limited to just pairs of organs, and in addition to organ-organ crosstalk, there are also organ-system and organ-body interactions. For instance, heart failure broadly impacts various organs and systems, including the kidney, liver, lung, and nervous system. Conversely, systemic dysregulation of metabolism, immunity, and nervous system activity greatly affects heart failure development and prognosis. This is particularly noteworthy, as more and more patients present with two or more coexisting chronic diseases or conditions (multimorbidity) due in part to the aging of society. Advances in treatment also contribute to the increase in multimorbidity, as exemplified by cardiovascular disease in cancer survivors. To understand the mechanisms underlying the increasing burden of multimorbidity, it is vital to elucidate the multilevel crosstalk and communication within the body at the levels of organ systems, tissues, and cells. In this article, we focus on chronic inflammation as a key common pathological basis of cardiovascular and metabolic diseases, and discuss emerging mechanisms that drive chronic inflammation in the context of multimorbidity.
Collapse
Affiliation(s)
- Yumiko Oishi
- Department of Biochemistry and Molecular Biology, Nippon Medical School, Tokyo, Japan
| | - Ichiro Manabe
- Department of Disease Biology and Molecular Medicine, Chiba University Graduate School of Medicine, Chiba, Japan
| |
Collapse
|
271
|
Shang D, Wang L, Klionsky DJ, Cheng H, Zhou R. Sex differences in autophagy-mediated diseases: toward precision medicine. Autophagy 2020; 17:1065-1076. [PMID: 32264724 DOI: 10.1080/15548627.2020.1752511] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Nearly all diseases in humans, to a certain extent, exhibit sex differences, including differences in the onset, progression, prevention, therapy, and prognosis of diseases. Accumulating evidence shows that macroautophagy/autophagy, as a mechanism for development, differentiation, survival, and homeostasis, is involved in numerous aspects of sex differences in diseases such as cancer, neurodegeneration, and cardiovascular diseases. Advances in our knowledge regarding sex differences in autophagy-mediated diseases have enabled an understanding of their roles in human diseases, although the underlying molecular mechanisms of sex differences in autophagy remain largely unexplored. In this review, we discuss current advances in our insight into the biology of sex differences in autophagy and disease, information that will facilitate precision medicine.Abbreviations: AD: Azheimer disease; AMBRA1: autophagy and beclin 1 regulator 1; APP: amyloid beta precursor protein; AR: androgen receptor; AMPK: AMP-activated protein kinase; ATG: autophagy related; ATP6AP2: ATPase H+ transporting accessory protein 2; BCL2L1: BCL2 like 1; BECN1: beclin 1; CTSD: cathepsin D; CYP19A1: cytochrome P450 family 19 subfamily A member 1; DSD: disorders of sex development; eALDI: enhancer alternate long-distance initiator; ESR1: estrogen receptor 1; ESR2: estrogen receptor 2; FYCO1: FYVE and coiled-coil domain autophagy adaptor 1; GABARAP: GABA type A receptor-associated protein; GLA: galactosidase alpha; GTEx: genotype-tissue expression; HDAC6: histone deacetylase 6; I-R: ischemia-reperfusion; LAMP2: lysosomal associated membrane protein 2; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; MTOR: mechanistic target of rapamycin kinase; m6A: N6-methyladenosine; MYBL2: MYB proto-oncogene like 2; PIK3C3: phosphatidylinositol 3-kinase catalytic subunit type 3; PSEN1: presenilin 1; PSEN2: presenilin 2; RAB9A, RAB9A: member RAS oncogene family; RAB9B, RAB9B: member RAS oncogene family; RAB40AL: RAB40A like; SF1: splicing factor 1; SOX9: SRY-box transcription factor 9; SRY: sex determining region Y; TFEB: transcription factor EB; ULK1: unc-51 like autophagy activating kinase 1; UVRAG: UV radiation resistance associated; VDAC2: voltage dependent anion channel 2; WDR45: WD repeat domain 45; XPDS: X-linked parkinsonism and spasticity; YTHDF2: YTH N6-methyladenosine RNA binding protein 2.
Collapse
Affiliation(s)
- Dangtong Shang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan, China
| | - Lingling Wang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan, China
| | - Daniel J Klionsky
- Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Hanhua Cheng
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan, China
| | - Rongjia Zhou
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan, China.,Department of Neurology, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, China
| |
Collapse
|
272
|
Ruan Y, Wang H, Chen B, Wen H, Wu CI. Mutations Beget More Mutations-Rapid Evolution of Mutation Rate in Response to the Risk of Runaway Accumulation. Mol Biol Evol 2020; 37:1007-1019. [PMID: 31778175 DOI: 10.1093/molbev/msz283] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The rapidity with which the mutation rate evolves could greatly impact evolutionary patterns. Nevertheless, most studies simply assume a constant rate in the time scale of interest (Kimura 1983; Drake 1991; Kumar 2005; Li 2007; Lynch 2010). In contrast, recent studies of somatic mutations suggest that the mutation rate may vary by several orders of magnitude within a lifetime (Kandoth et al. 2013; Lawrence et al. 2013). To resolve the discrepancy, we now propose a runaway model, applicable to both the germline and soma, whereby mutator mutations form a positive-feedback loop. In this loop, any mutator mutation would increase the rate of acquiring the next mutator, thus triggering a runaway escalation in mutation rate. The process can be initiated more readily if there are many weak mutators than a few strong ones. Interestingly, even a small increase in the mutation rate at birth could trigger the runaway process, resulting in unfit progeny. In slowly reproducing species, the need to minimize the risk of this uncontrolled accumulation would thus favor setting the mutation rate low. In comparison, species that starts and ends reproduction sooner do not face the risk and may set the baseline mutation rate higher. The mutation rate would evolve in response to the risk of runaway mutation, in particular, when the generation time changes. A rapidly evolving mutation rate may shed new lights on many evolutionary phenomena (Elango et al. 2006; Thomas et al. 2010, 2018; Langergraber et al. 2012; Besenbacher et al. 2019).
Collapse
Affiliation(s)
- Yongsen Ruan
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Haiyu Wang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Bingjie Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Haijun Wen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Chung-I Wu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.,CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,Department of Ecology and Evolution, University of Chicago, Chicago, IL
| |
Collapse
|
273
|
Affiliation(s)
- Christina Curtis
- Departments of Medicine and Genetics, Stanford University School of Medicine, Lorry Lokey Stem Cell Research Building, Stanford, CA 94305, USA.
| |
Collapse
|
274
|
Abstract
Ultraviolet (UV) irradiation causes various types of DNA damage, which leads to specific mutations and the emergence of skin cancer in humans, often decades after initial exposure. Different UV wavelengths cause the formation of prominent UV-induced DNA lesions. Most of these lesions are removed by the nucleotide excision repair pathway, which is defective in rare genetic skin disorders referred to as xeroderma pigmentosum. A major role in inducing sunlight-dependent skin cancer mutations is assigned to the cyclobutane pyrimidine dimers (CPDs). In this review, we discuss the mechanisms of UV damage induction, the genomic distribution of this damage, relevant DNA repair mechanisms, the proposed mechanisms of how UV-induced CPDs bring about DNA replication-dependent mutagenicity in mammalian cells, and the strong signature of UV damage and mutagenesis found in skin cancer genomes.
Collapse
|
275
|
Abstract
The remarkable success of cancer immunotherapies, especially the checkpoint blocking antibodies, in a subset of patients has reinvigorated the study of tumor-immune crosstalk and its role in heterogeneity of response. High-throughput sequencing and imaging technologies can help recapitulate various aspects of the tumor ecosystem. Computational approaches provide an arsenal of tools to efficiently analyze, quantify and integrate multiple parameters of tumor immunity mined from these diverse but complementary high-throughput datasets. This chapter describes numerous such computational approaches in tumor immunology that leverage high-throughput data from diverse sources (genomic, transcriptomics, epigenomics and digitized histopathology images) to systematically interrogate tumor immunity in context of its microenvironment, and to identify mechanisms that confer resistance or sensitivity to cancer therapies, in particular immunotherapy.
Collapse
|
276
|
Shen Y, Ha W, Zeng W, Queen D, Liu L. Exome sequencing identifies novel mutation signatures of UV radiation and trichostatin A in primary human keratinocytes. Sci Rep 2020; 10:4943. [PMID: 32188867 PMCID: PMC7080724 DOI: 10.1038/s41598-020-61807-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 03/03/2020] [Indexed: 12/03/2022] Open
Abstract
Canonical ultraviolet (UV) mutation type and spectra are traditionally defined by direct sequencing-based approaches to map mutations in a limited number of representative DNA elements. To obtain an unbiased view of genome wide UV mutation features, we performed whole exome-sequencing (WES) to profile single nucleotide substitutions in UVB-irradiated primary human keratinocytes. Cross comparison of UV mutation profiles under different UVB radiation conditions revealed that T > C transition was highly prevalent in addition to C > T transition. We also identified 5'-ACG-3' as a common sequence motif of C > T transition. Furthermore, our analyses uncovered several recurring UV mutations following acute UVB radiation affecting multiple genes including HRNR, TRIOBP, KCNJ12, and KMT2C, which are frequently mutated in skin cancers, indicating their potential role as founding mutations in UV-induced skin tumorigenesis. Pretreatment with trichostatin A, a pan-histone deacetylase inhibitor that renders chromatin decondensation, significantly decreased the number of mutations in UVB-irradiated keratinocytes. Unexpectedly, we found trichostatin A to be a mutagen that caused DNA damage and mutagenesis at least partly through increased reactive oxidation. In summary, our study reveals new UV mutation features following acute UVB radiation and identifies novel UV mutation hotspots that may potentially represent founding driver mutations in skin cancer development.
Collapse
Affiliation(s)
- Yao Shen
- Department of Systems Biology, Columbia University, New York, New York, USA
| | - Wootae Ha
- The Hormel Institute, University of Minnesota, Austin, MN, USA
| | - Wangyong Zeng
- Department of Dermatology, Columbia University, New York, USA
| | - Dawn Queen
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, 10032, USA
| | - Liang Liu
- The Hormel Institute, University of Minnesota, Austin, MN, USA.
- Department of Dermatology, Columbia University, New York, USA.
| |
Collapse
|
277
|
Wu J, Hu S, Zhang L, Xin J, Sun C, Wang L, Ding K, Wang B. Tumor circulome in the liquid biopsies for cancer diagnosis and prognosis. Theranostics 2020; 10:4544-4556. [PMID: 32292514 PMCID: PMC7150480 DOI: 10.7150/thno.40532] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 01/07/2020] [Indexed: 12/20/2022] Open
Abstract
Liquid biopsy is a convenient, fast, non-invasive and reproducible sampling method that can dynamically reflect the changes in tumor gene expression profile, and provide a robust basis for individualized therapy and early diagnosis of cancer. Circulating tumor DNA (ctDNA) and circulating tumor cells (CTCs) are the currently approved diagnostic biomarkers for screening cancer patients. In addition, tumor-derived extracellular vesicles (tdEVs), circulating tumor-derived proteins, circulating tumor RNA (ctRNA) and tumor-bearing platelets (TEPs) are other components of liquid biopsies with diagnostic potential. In this review, we have discussed the clinical applications of these biomarkers, and the factors that limit their implementation in routine clinical practice. In addition, the most recent developments in the isolation and analysis of circulating tumor biomarkers have been summarized, and the potential of non-blood liquid biopsies in tumor diagnostics has also been discussed.
Collapse
Affiliation(s)
- Jicheng Wu
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
- Institute of Translational Medicine, Zhejiang University, Hangzhou 310029, China
| | - Shen Hu
- Department of Obstetrics, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Lihong Zhang
- Department of Biochemistry, College of Biomedical Sciences, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Jinxia Xin
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
- Institute of Translational Medicine, Zhejiang University, Hangzhou 310029, China
| | - Chongran Sun
- Department of Neurosurgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Liquan Wang
- Department of Obstetrics, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Kefeng Ding
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Ben Wang
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
- Institute of Translational Medicine, Zhejiang University, Hangzhou 310029, China
| |
Collapse
|
278
|
Seyfried TN, Mukherjee P, Iyikesici MS, Slocum A, Kalamian M, Spinosa JP, Chinopoulos C. Consideration of Ketogenic Metabolic Therapy as a Complementary or Alternative Approach for Managing Breast Cancer. Front Nutr 2020; 7:21. [PMID: 32219096 PMCID: PMC7078107 DOI: 10.3389/fnut.2020.00021] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 02/21/2020] [Indexed: 12/14/2022] Open
Abstract
Breast cancer remains as a significant cause of morbidity and mortality in women. Ultrastructural and biochemical evidence from breast biopsy tissue and cancer cells shows mitochondrial abnormalities that are incompatible with energy production through oxidative phosphorylation (OxPhos). Consequently, breast cancer, like most cancers, will become more reliant on substrate level phosphorylation (fermentation) than on oxidative phosphorylation (OxPhos) for growth consistent with the mitochondrial metabolic theory of cancer. Glucose and glutamine are the prime fermentable fuels that underlie therapy resistance and drive breast cancer growth through substrate level phosphorylation (SLP) in both the cytoplasm (Warburg effect) and the mitochondria (Q-effect), respectively. Emerging evidence indicates that ketogenic metabolic therapy (KMT) can reduce glucose availability to tumor cells while simultaneously elevating ketone bodies, a non-fermentable metabolic fuel. It is suggested that KMT would be most effective when used together with glutamine targeting. Information is reviewed for suggesting how KMT could reduce systemic inflammation and target tumor cells without causing damage to normal cells. Implementation of KMT in the clinic could improve progression free and overall survival for patients with breast cancer.
Collapse
Affiliation(s)
| | - Purna Mukherjee
- Biology Department, Boston College, Chestnut Hill, MA, United States
| | - Mehmet S. Iyikesici
- Medical Oncology, Kemerburgaz University Bahcelievler Medical Park Hospital, Istanbul, Turkey
| | - Abdul Slocum
- Medical Oncology, Chemo Thermia Oncology Center, Istanbul, Turkey
| | | | | | | |
Collapse
|
279
|
Janiszewska M. The microcosmos of intratumor heterogeneity: the space-time of cancer evolution. Oncogene 2020; 39:2031-2039. [PMID: 31784650 PMCID: PMC7374939 DOI: 10.1038/s41388-019-1127-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 11/15/2019] [Accepted: 11/20/2019] [Indexed: 12/17/2022]
Abstract
The Cancer Genome Atlas consortium brought us terabytes of information about genetic alterations in different types of human tumors. While many cancer-driver genes have been identified through these efforts, interrogating cancer genomes has also shed new light on tumor complexity. Mutations were found to vary tremendously in their allelic frequencies within the same tumor. Based on those variant allelic frequencies grouping, an estimate of genetically distinct "clones" of cancer cells can be determined for each tumor. It was estimated that 4-8 clones are present in every human tumor. Presence of distinct clones, cells that differ in their genotype and/or phenotype, is one of the roots for the major challenge of effectively curing cancer patients. Any given treatment applied to a heterogeneous mixture of cancer cells will yield distinct responses in different cells and may be ineffective in killing particular clones. Moreover, in highly heterogeneous tumors, stochastically, there is a higher chance of presence of traits, such as point mutations in key receptor tyrosine kinases, that drive drug resistance. Thus, intratumor heterogeneity is like an arsenal, providing a variety of weapons for self-defense against cancer-targeted therapy. However, in this arsenal the supplies are constantly changing, as cancer cells are accumulating new mutations. What is also changing is the battlefield-the tumor microenvironment including all noncancerous cells within the tumor and surrounding tissue, which also contribute to the diversification of cancer's forces. In order to design more effective therapies that would target this ever-changing landscape, we need to learn more about the two elusive variables that shape the tumor ecosystem: the space-how could we exploit the organization of tumor microenvironment? and the time-how could we predict the changes in heterogeneous tumors?
Collapse
Affiliation(s)
- Michalina Janiszewska
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA.
| |
Collapse
|
280
|
Freeman TM, Wang D, Harris J. Genomic loci susceptible to systematic sequencing bias in clinical whole genomes. Genome Res 2020; 30:415-426. [PMID: 32156711 PMCID: PMC7111519 DOI: 10.1101/gr.255349.119] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 02/14/2020] [Indexed: 11/26/2022]
Abstract
Accurate massively parallel sequencing (MPS) of genetic variants is key to many areas of science and medicine, such as cataloging population genetic variation and diagnosing genetic diseases. Certain genomic positions can be prone to higher rates of systematic sequencing and alignment bias that limit accuracy, resulting in false positive variant calls. Current standard practices to differentiate between loci that can and cannot be sequenced with high confidence utilize consensus between different sequencing methods as a proxy for sequencing confidence. These practices have significant limitations, and alternative methods are required to overcome them. We have developed a novel statistical method based on summarizing sequenced reads from whole-genome clinical samples and cataloging them in "Incremental Databases" that maintain individual confidentiality. Allele statistics were cataloged for each genomic position that consistently showed systematic biases with the corresponding MPS sequencing pipeline. We found systematic biases present at ∼1%-3% of the human autosomal genome across five patient cohorts. We identified which genomic regions were more or less prone to systematic biases, including large homopolymer flanks (odds ratio = 23.29-33.69) and the NIST high confidence genomic regions (odds ratio = 0.154-0.191). We confirmed our predictions on a gold-standard reference genome and showed that these systematic biases can lead to suspect variant calls within clinical panels. Our results recommend increased caution to address systematic biases in whole-genome sequencing and alignment. This study provides the implementation of a simple statistical approach to enhance quality control of clinically sequenced samples by flagging variants at suspect loci for further analysis or exclusion.
Collapse
Affiliation(s)
- Timothy M Freeman
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield S10 2HQ, United Kingdom
| | - Dennis Wang
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield S10 2HQ, United Kingdom
- NIHR Sheffield Biomedical Research Centre, Sheffield S10 2JF, United Kingdom
- Department of Computer Science, University of Sheffield, Sheffield S1 4DP, United Kingdom
| | - Jason Harris
- Personalis, Incorporated, Menlo Park, California 94025, USA
| |
Collapse
|
281
|
Yura Y, Sano S, Walsh K. Clonal Hematopoiesis: A New Step Linking Inflammation to Heart Failure. JACC Basic Transl Sci 2020; 5:196-207. [PMID: 32140625 PMCID: PMC7046537 DOI: 10.1016/j.jacbts.2019.08.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 08/19/2019] [Indexed: 12/17/2022]
Abstract
Heart failure is a common disease with poor prognosis that is associated with cardiac immune cell infiltration and dysregulated cytokine expression. Recently, the clonal expansion of hematopoietic cells with acquired (i.e., nonheritable) DNA mutations, a process referred to as clonal hematopoiesis, has been reported to be associated with cardiovascular diseases including heart failure. Mechanistic studies have shown that leukocytes that harbor these somatic mutations display altered inflammatory characteristics that worsen the phenotypes associated with heart failure in experimental models. In this review, we summarize recent epidemiological and experimental evidence that support the hypothesis that clonal hematopoiesis-mediated immune cell dysfunction contributes to heart failure and cardiovascular disease in general.
Collapse
Key Words
- ASXL1, additional sex combs like 1
- DNMT3A
- DNMT3A, DNA methyltransferase-3A
- HSPCs, hematopoietic stem and progenitor cells
- IL, interleukin
- Il-1β inflammasome
- JAK2
- JAK2, janus kinase 2
- MPN, myeloproliferative neoplasm
- PPM1D, protein phosphatase, Mg2+/Mn2+ dependent 1D
- TET2
- TET2, ten-eleven translocation-2
- TNF, tumor necrosis factor
- TNF-α
- TP53, tumor protein 53
- VAF, variant allele fraction
- hsCRP, high-sensitivity C-reactive protein
Collapse
Affiliation(s)
- Yoshimitsu Yura
- Hematovascular Biology Center and the Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Soichi Sano
- Hematovascular Biology Center and the Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Kenneth Walsh
- Hematovascular Biology Center and the Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, Virginia
| |
Collapse
|
282
|
Adashek JJ, Kato S, Lippman SM, Kurzrock R. The paradox of cancer genes in non-malignant conditions: implications for precision medicine. Genome Med 2020; 12:16. [PMID: 32066498 PMCID: PMC7027240 DOI: 10.1186/s13073-020-0714-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 01/30/2020] [Indexed: 02/07/2023] Open
Abstract
Next-generation sequencing has enabled patient selection for targeted drugs, some of which have shown remarkable efficacy in cancers that have the cognate molecular signatures. Intriguingly, rapidly emerging data indicate that altered genes representing oncogenic drivers can also be found in sporadic non-malignant conditions, some of which have negligible and/or low potential for transformation to cancer. For instance, activating KRAS mutations are discerned in endometriosis and in brain arteriovenous malformations, inactivating TP53 tumor suppressor mutations in rheumatoid arthritis synovium, and AKT, MAPK, and AMPK pathway gene alterations in the brains of Alzheimer's disease patients. Furthermore, these types of alterations may also characterize hereditary conditions that result in diverse disabilities and that are associated with a range of lifetime susceptibility to the development of cancer, varying from near universal to no elevated risk. Very recently, the repurposing of targeted cancer drugs for non-malignant conditions that are associated with these genomic alterations has yielded therapeutic successes. For instance, the phenotypic manifestations of CLOVES syndrome, which is characterized by tissue overgrowth and complex vascular anomalies that result from the activation of PIK3CA mutations, can be ameliorated by the PIK3CA inhibitor alpelisib, which was developed and approved for breast cancer. In this review, we discuss the profound implications of finding molecular alterations in non-malignant conditions that are indistinguishable from those driving cancers, with respect to our understanding of the genomic basis of medicine, the potential confounding effects in early cancer detection that relies on sensitive blood tests for oncogenic mutations, and the possibility of reverse repurposing drugs that are used in oncology in order to ameliorate non-malignant illnesses and/or to prevent the emergence of cancer.
Collapse
Affiliation(s)
- Jacob J Adashek
- Department of Internal Medicine, University of South Florida, H Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Shumei Kato
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, University of California San Diego Moores Cancer Center, Health Sciences Drive, La Jolla, CA, 92093, USA
| | - Scott M Lippman
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, University of California San Diego Moores Cancer Center, Health Sciences Drive, La Jolla, CA, 92093, USA
| | - Razelle Kurzrock
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, University of California San Diego Moores Cancer Center, Health Sciences Drive, La Jolla, CA, 92093, USA.
| |
Collapse
|
283
|
Amorós-Pérez M, Fuster JJ. Clonal hematopoiesis driven by somatic mutations: A new player in atherosclerotic cardiovascular disease. Atherosclerosis 2020; 297:120-126. [PMID: 32109665 DOI: 10.1016/j.atherosclerosis.2020.02.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 02/06/2020] [Accepted: 02/12/2020] [Indexed: 02/06/2023]
Abstract
The accumulation of acquired mutations is an inevitable consequence of the aging process, but its pathophysiological relevance has remained largely unexplored beyond cancer. Most of these mutations have little or no functional consequences, but in a few rare instances, a mutation may arise that confers a competitive advantage to a stem cell, leading to its clonal expansion. When such a mutation occurs in hematopoietic stem cells, it leads to a situation of clonal hematopoiesis, which has the potential to affect multiple tissues beyond the bone marrow, as the clonal expansion of the mutant stem cell is extended to circulating blood cells and tissue-infiltrating immune cells. Recent genomics and experimental studies have provided support to the notion that this somatic mutation-driven clonal hematopoiesis contributes to vascular inflammation and the development of atherosclerosis and related cardiovascular and cerebrovascular ischemic events. Here, we review our current understanding of this emerging cardiovascular risk modifier and the mechanisms underlying its connection to atherosclerosis development.
Collapse
Affiliation(s)
- Marta Amorós-Pérez
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - José J Fuster
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain.
| |
Collapse
|
284
|
Rafaeva M, Erler JT. Framing cancer progression: influence of the organ- and tumour-specific matrisome. FEBS J 2020; 287:1454-1477. [PMID: 31972068 DOI: 10.1111/febs.15223] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 12/16/2019] [Accepted: 01/20/2020] [Indexed: 12/19/2022]
Abstract
The extracellular matrix (ECM) plays a crucial role in regulating organ homeostasis. It provides mechanical and biochemical cues directing cellular behaviour and, therefore, has control over the progression of diseases such as cancer. Recent efforts have greatly enhanced our knowledge of the protein composition of the ECM and its regulators, the so-called matrisome, in healthy and cancerous tissues; yet, an overview of the common signatures and organ-specific ECM in cancer is missing. Here, we address this by taking a detailed approach to review why cancer grows in certain organs, and focus on the influence of the matrisome at primary and metastatic tumour sites. Our in-depth and comprehensive review of the current literature and general understanding identifies important commonalities and distinctions, providing insight into the biology of metastasis, which could pave the way to improve future diagnostics and therapies.
Collapse
Affiliation(s)
- Maria Rafaeva
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen (UCPH), Denmark
| | - Janine T Erler
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen (UCPH), Denmark
| |
Collapse
|
285
|
Yoshida K, Gowers KHC, Lee-Six H, Chandrasekharan DP, Coorens T, Maughan EF, Beal K, Menzies A, Millar FR, Anderson E, Clarke SE, Pennycuick A, Thakrar RM, Butler CR, Kakiuchi N, Hirano T, Hynds RE, Stratton MR, Martincorena I, Janes SM, Campbell PJ. Tobacco smoking and somatic mutations in human bronchial epithelium. Nature 2020; 578:266-272. [PMID: 31996850 PMCID: PMC7021511 DOI: 10.1038/s41586-020-1961-1] [Citation(s) in RCA: 291] [Impact Index Per Article: 72.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 12/29/2019] [Indexed: 01/06/2023]
Abstract
Tobacco smoking causes lung cancer1-3, a process that is driven by more than 60 carcinogens in cigarette smoke that directly damage and mutate DNA4,5. The profound effects of tobacco on the genome of lung cancer cells are well-documented6-10, but equivalent data for normal bronchial cells are lacking. Here we sequenced whole genomes of 632 colonies derived from single bronchial epithelial cells across 16 subjects. Tobacco smoking was the major influence on mutational burden, typically adding from 1,000 to 10,000 mutations per cell; massively increasing the variance both within and between subjects; and generating several distinct mutational signatures of substitutions and of insertions and deletions. A population of cells in individuals with a history of smoking had mutational burdens that were equivalent to those expected for people who had never smoked: these cells had less damage from tobacco-specific mutational processes, were fourfold more frequent in ex-smokers than current smokers and had considerably longer telomeres than their more-mutated counterparts. Driver mutations increased in frequency with age, affecting 4-14% of cells in middle-aged subjects who had never smoked. In current smokers, at least 25% of cells carried driver mutations and 0-6% of cells had two or even three drivers. Thus, tobacco smoking increases mutational burden, cell-to-cell heterogeneity and driver mutations, but quitting promotes replenishment of the bronchial epithelium from mitotically quiescent cells that have avoided tobacco mutagenesis.
Collapse
Affiliation(s)
- Kenichi Yoshida
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Kate H C Gowers
- Lungs For Living Research Centre, UCL Respiratory, University College London, London, UK
| | - Henry Lee-Six
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Tim Coorens
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Elizabeth F Maughan
- Lungs For Living Research Centre, UCL Respiratory, University College London, London, UK
| | - Kathryn Beal
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Andrew Menzies
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Fraser R Millar
- Lungs For Living Research Centre, UCL Respiratory, University College London, London, UK
| | | | - Sarah E Clarke
- Lungs For Living Research Centre, UCL Respiratory, University College London, London, UK
| | - Adam Pennycuick
- Lungs For Living Research Centre, UCL Respiratory, University College London, London, UK
| | - Ricky M Thakrar
- Lungs For Living Research Centre, UCL Respiratory, University College London, London, UK
- Department of Thoracic Medicine, University College London Hospital, London, UK
| | - Colin R Butler
- Lungs For Living Research Centre, UCL Respiratory, University College London, London, UK
- Department of Thoracic Medicine, University College London Hospital, London, UK
| | - Nobuyuki Kakiuchi
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Tomonori Hirano
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Robert E Hynds
- Lungs For Living Research Centre, UCL Respiratory, University College London, London, UK
- CRUK Lung Cancer Centre of Excellence, UCL Cancer Institute, University College London, London, UK
| | | | | | - Sam M Janes
- Lungs For Living Research Centre, UCL Respiratory, University College London, London, UK.
- Department of Thoracic Medicine, University College London Hospital, London, UK.
| | - Peter J Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK.
- Stem Cell Institute, University of Cambridge, Cambridge, UK.
| |
Collapse
|
286
|
Liu J. The "life code": A theory that unifies the human life cycle and the origin of human tumors. Semin Cancer Biol 2020; 60:380-397. [PMID: 31521747 DOI: 10.1016/j.semcancer.2019.09.005] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 09/03/2019] [Accepted: 09/09/2019] [Indexed: 02/07/2023]
Abstract
Tumors arise from the transformation of normal stem cells or mature somatic cells. Intriguingly, two types of tumors have been observed by pathologists for centuries: well-differentiated tumors and undifferentiated tumors. Well-differentiated tumors are architecturally similar to the tissues from which they originate, whereas undifferentiated tumors exhibit high nuclear atypia and do not resemble their tissue of origin. The relationship between these two tumor types and the human life cycle has not been clear. Here I propose a unifying theory that explains the processes of transformation of both tumor types with our life cycle. Human life starts with fertilization of an egg by a sperm to form a zygote. The zygote undergoes successive rounds of cleavage division to form blastomeres within the zona pellucida, with progressive decreases in cell size, and the cleaved blastomeres then compact to form a 32-cell or a "64n" morula [n = 1 full set of chromosomes]. Thus early embryogenesis can be interpreted as a progressive increase in ploidy, and if the zona pellucida is considered a cell membrane and cleavage is interpreted as endomitosis, then the 32-cell morula can be considered a multinucleated giant cell (or 64n syncytium). The decrease in cell size is accompanied by an increase in the nuclear-to-cytoplasmic (N/C) ratio, which then selectively activates a combined set of embryonic transcription factors that dedifferentiate the parental genome to a zygotic genome. This process is associated with a morphologic transition from a morula to a blastocyst and formation of an inner cell mass that gives rise to a new embryonic life. If the subsequent differentiation proceeds to complete maturation, then a normal life results. However, if differentiation is blocked at any point along the continuum of primordial germ cell to embryonic maturation to fetal organ maturation, a well-differentiated tumor will develop. Depending on the level of developmental hierarchy at which the stem cell differentiation is blocked, the resulting tumor can range from highly malignant to benign. Undifferentiated tumors are derived from mature somatic cells through dedifferentiation via a recently described reprogramming mechanism named the giant cell life cycle or the giant cell cycle. This mechanism can initiate "somatic embryogenesis" via an increase in ploidy ranging from 4n to 64n or more, similar to that in normal embryogenesis. This dedifferentiation mechanism is initiated through an endocycle and is followed by endomitosis, which leads to the formation of mononucleated or multinucleated polyploid giant cancer cells (PGCCs), that is, cancer stem-like cells that mimic the blastomere-stage embryo. The giant cell life cycle leads to progressive increases in the N/C ratio and awakens the suppressed embryonic reprogram, resulting in mature somatic transformation into undifferentiated tumors. Thus, the increase in ploidy explains not only normal embryogenesis for well-differentiated tumors but also "somatic embryogenesis" for undifferentiated tumors. I refer to this ploidy increase as the 'life code". The concept of the "life code" may provide a simple theoretical framework to guide our immense efforts to understand cancer and fight this disease.
Collapse
Affiliation(s)
- Jinsong Liu
- Department of Anatomic Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, United States.
| |
Collapse
|
287
|
Wu Z, Long X, Tsang SY, Hu T, Yang JF, Mat WK, Wang H, Xue H. Genomic subtyping of liver cancers with prognostic application. BMC Cancer 2020; 20:84. [PMID: 32005109 PMCID: PMC6995214 DOI: 10.1186/s12885-020-6546-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 01/15/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Cancer subtyping has mainly relied on pathological and molecular means. Massively parallel sequencing-enabled subtyping requires genomic markers to be developed based on global features rather than individual mutations for effective implementation. METHODS In the present study, the whole genome sequences (WGS) of 110 liver cancers of Japanese patients published with different pathologies were analyzed with respect to their single nucleotide variations (SNVs) comprising both gain-of-heterozygosity (GOH) and loss-of-heterozygosity (LOH) mutations, the signatures of combined GOH and LOH mutations, along with recurrent copy number variations (CNVs). RESULTS The results, obtained based on the WGS sequences as well as the Exome subset within the WGSs that covered ~ 2.0% of the WGS and the AluScan-subset within the WGSs that were amplifiable by Alu element-consensus primers and covered ~ 2.1% of the WGS, indicated that the WGS samples could be employed with the mutational parameters of SNV load, LOH%, the Signature α%, and survival-associated recurrent CNVs (srCNVs) as genomic markers for subtyping to stratify liver cancer patients prognostically into the long and short survival subgroups. The usage of the AluScan-subset data, which could be implemented with sub-micrograms of DNA samples and vastly reduced sequencing analysis task, outperformed the usage of WGS data when LOH% was employed as stratifying criterion. CONCLUSIONS Thus genomic subtyping performed with novel genomic markers identified in this study was effective in predicting patient-survival duration, with cohorts of hepatocellular carcinomas alone and those including intrahepatic cholangiocarcinomas. Such relatively heterogeneity-insensitive genomic subtyping merits further studies with a broader spectrum of cancers.
Collapse
Affiliation(s)
- Zhenggang Wu
- HKUST Shenzhen Research Institute, 9 Yuexing First Road, Nanshan, Shenzhen, China.,Division of Life Science and Applied Genomics Center, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Xi Long
- Division of Life Science and Applied Genomics Center, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Shui Ying Tsang
- Division of Life Science and Applied Genomics Center, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Taobo Hu
- Division of Life Science and Applied Genomics Center, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Jian-Feng Yang
- Division of Life Science and Applied Genomics Center, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Wai Kin Mat
- Division of Life Science and Applied Genomics Center, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Hongyang Wang
- Eastern Hepatobiliary Surgery Institute, Second Military Medical University, Shanghai, China.
| | - Hong Xue
- HKUST Shenzhen Research Institute, 9 Yuexing First Road, Nanshan, Shenzhen, China. .,Division of Life Science and Applied Genomics Center, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China. .,Center for Cancer Genomics, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China. .,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China. .,Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.
| |
Collapse
|
288
|
Ayachi S, Buscarlet M, Busque L. 60 Years of clonal hematopoiesis research: From X-chromosome inactivation studies to the identification of driver mutations. Exp Hematol 2020; 83:2-11. [PMID: 32001340 DOI: 10.1016/j.exphem.2020.01.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/18/2020] [Accepted: 01/22/2020] [Indexed: 12/17/2022]
Abstract
The history of clonal hematopoiesis (CH) research is punctuated by several seminal discoveries that have forged our understanding of cancer development. The clever application of the principle of random X-chromosome inactivation (XCI) in females led to the development of the first test to identify clonal derivation of cells. Initially limited by a low level of informativeness, the applicability of these assays expanded with differential methylation-based assays at highly polymorphic genes such as the human androgen receptor (HUMARA). Twenty years ago, the observation that skewing of XCI ratios increases as women age was the first clue that led to the identification of mutations in the TET2 gene in hematologically normal aging individuals. In 2014, large-scale genomic approaches of three cohorts allowed definition of CH, which was reported to increase the risk of developing hematologic cancers and cardiovascular diseases. These observations created a fertile field of investigation aimed at investigating the etiology and consequences of CH. The most frequently mutated genes in CH are DNMT3A, TET2, and ASXL1, which have a role in hematopoietic stem cell (HSC) development and self-renewal. These mutations confer a competitive advantage to the CH clones. However, the penetrance of CH is age dependent but incomplete, suggesting the influence of extrinsic factors. Recent data attribute a modest role to genetic predisposition, but several observations point to the impact of a pro-inflammatory milieu that advantages the mutated clones. CH may be a barometer of nonhealthy aging, and interventions devised at curbing its initiation or progression should be a research priority.
Collapse
Affiliation(s)
- Sami Ayachi
- Research Center, Hôpital Maisonneuve-Rosemont, Montréal, Québec, Canada; Department of Medicine, Université de Montréal, Montreal, Québec, Canada
| | - Manuel Buscarlet
- Research Center, Hôpital Maisonneuve-Rosemont, Montréal, Québec, Canada
| | - Lambert Busque
- Research Center, Hôpital Maisonneuve-Rosemont, Montréal, Québec, Canada; Department of Medicine, Université de Montréal, Montreal, Québec, Canada; Hematology Division, Hôpital Maisonneuve-Rosemont, Montréal, Québec, Canada.
| |
Collapse
|
289
|
Zohn IE. Hsp90 and complex birth defects: A plausible mechanism for the interaction of genes and environment. Neurosci Lett 2020; 716:134680. [PMID: 31821846 DOI: 10.1016/j.neulet.2019.134680] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 12/04/2019] [Accepted: 12/06/2019] [Indexed: 12/17/2022]
Abstract
How genes and environment interact to cause birth defects is not well understood, but key to developing new strategies to modify risk. The threshold model has been proposed to represent this complex interaction. This model stipulates that while environmental exposure or genetic mutation alone may not result in a defect, factors in combination increase phenotypic variability resulting in more individuals crossing the disease threshold where birth defects manifest. Many environmental factors that contribute to birth defects induce widespread cellular stress and misfolding of proteins. Yet, the impact of the stress response on the threshold model is not typically considered in discephering the etiology of birth defects. This mini-review will explore a potential mechanism for gene-environment interactions co-opted from studies of evolution. This model stipulates that heat shock proteins that mediate the stress response induced by environmental factors can influence the number of individuals that cross disease thresholds resulting in increased incidence of birth defects. Studies in the field of evolutionary biology have demonstrated that heat shock proteins and Hsp90 in particular provide a link between environmental stress, genotype and phenotype. Hsp90 is a highly expressed molecular chaperone that assists a wide variety of protein clients with folding and conformational changes needed for proper function. Hsp90 also chaperones client proteins with potentially deleterious amino acid changes to suppress variation caused by genetic mutations. However, upon exposure to stress, Hsp90 abandons its normal physiological clients and is diverted to assist with the misfolded protein response. This can impact the activity of signaling pathways that involve Hsp90 clients as well as unmask suppressed protein variation, essentially creating complex traits in a single step. In this capacity Hsp90 acts as an evolutionary capacitor allowing stored variation to accumulate and then become expressed in times of stress. This mechanism provides a substrate which natural selection can act upon at the population level allowing survival of the species with selective pressure. However, at the level of the individual, this mechanism can result in simultaneous expression of deleterious variants as well as reduced activity of a variety of Hsp90 chaperoned pathways, potentially shifting phenotypic variability over the disease threshold resulting in birth defects.
Collapse
Affiliation(s)
- Irene E Zohn
- Center for Genetic Medicine Research, Children's National Health System, Washington, DC, 20010, USA.
| |
Collapse
|
290
|
Abstract
Technological advances in the ability to read the human genome have accelerated the speed of sequencing, such that today we can perform whole genome sequencing (WGS) in one day. Until recently, genomic studies have largely been limited to seeking novel scientific discoveries. The application of new insights gained through cancer WGS into the clinical domain, have been relatively limited. Looking ahead, a vast amount of data can be generated by genomic studies. Of note, excellent organisation of genomic and clinical data permits the application of machine-learning methods which can lead to the development of clinical algorithms that could assist future clinicians and genomicists in the analysis and interpretation of individual cancer genomes. Here, we describe what can be gleaned from holistic whole cancer genome profiling and argue that we must build the infrastructure and educational frameworks to support the modern clinical genomicist to prepare for a future where WGS will be the norm.
Collapse
Affiliation(s)
- Serena Nik-Zainal
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, UK / Academic Laboratory of Medical Genetics, Addenbrookes Treatment Centre, Cambridge, UK
| | - Yasin Memari
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, UK / Academic Laboratory of Medical Genetics, Addenbrookes Treatment Centre, Cambridge, UK
| | - Helen R Davies
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, UK / Academic Laboratory of Medical Genetics, Addenbrookes Treatment Centre, Cambridge, UK
| |
Collapse
|
291
|
Fujino T, Kitamura T. ASXL1 mutation in clonal hematopoiesis. Exp Hematol 2020; 83:74-84. [PMID: 31945396 DOI: 10.1016/j.exphem.2020.01.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 01/04/2020] [Accepted: 01/06/2020] [Indexed: 12/13/2022]
Abstract
Recent advances in DNA sequencing technologies have enhanced our knowledge about several diseases. Coupled with easy accessibility to blood samples, hematology plays a leading role in understanding the process of carcinogenesis. Clonal hematopoiesis (CH) with somatic mutations is observed in at least 10% of people over 65 years of age, without apparent hematologic disorders. CH is associated with increased risk of hematologic malignancies, which is indicative of a pre-malignant condition. Therefore, a better understanding of CH will help elucidate the mechanism of multi-step tumorigenesis in the hematopoietic system. Somatic mutations of ASXL1 are frequently detected in CH and myeloid malignancies. Although ASXL1 does not have any catalytic activity, it is involved in multiple histone modifications including H3K4me3, H3K27me3, and H2AK119Ub, suggesting its function as a scaffolding protein. Most ASXL1 mutations detected in CH and myeloid malignancies are frameshift or nonsense mutations of the last exon, generating a C-terminally truncated protein. Deletion of Asxl1 or expression of mutant ASXL1 in mice alters histone modifications and facilitates aberrant gene expression, resulting in myeloid transformation. On the contrary, these mice exhibit impaired functioning of hematopoietic stem cells (HSCs), suggesting the negative effects of ASXL1 mutations on stem cell function. Thus, how ASXL1 mutations induce a clonal advantage of hematopoietic cells and subsequent CH development has not been elucidated. Here, we have reviewed the current literature that enhances our understanding of ASXL1, including its mutational landscape, function, and involvement of its mutation in pathogenesis of CH and myeloid malignancies. Finally, we discuss the potential causes of CH harboring ASXL1 mutations with our latest knowledge.
Collapse
Affiliation(s)
- Takeshi Fujino
- Division of Cellular Therapy, The Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Toshio Kitamura
- Division of Cellular Therapy, The Institute of Medical Science, University of Tokyo, Tokyo, Japan.
| |
Collapse
|
292
|
Heflich RH, Johnson GE, Zeller A, Marchetti F, Douglas GR, Witt KL, Gollapudi BB, White PA. Mutation as a Toxicological Endpoint for Regulatory Decision-Making. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:34-41. [PMID: 31600846 DOI: 10.1002/em.22338] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 09/09/2019] [Accepted: 09/14/2019] [Indexed: 05/23/2023]
Abstract
Mutations induced in somatic cells and germ cells are responsible for a variety of human diseases, and mutation per se has been considered an adverse health concern since the early part of the 20th Century. Although in vitro and in vivo somatic cell mutation data are most commonly used by regulatory agencies for hazard identification, that is, determining whether or not a substance is a potential mutagen and carcinogen, quantitative mutagenicity dose-response data are being used increasingly for risk assessments. Efforts are currently underway to both improve the measurement of mutations and to refine the computational methods used for evaluating mutation data. We recommend continuing the development of these approaches with the objective of establishing consensus regarding the value of including the quantitative analysis of mutation per se as a required endpoint for comprehensive assessments of toxicological risk. Environ. Mol. Mutagen. 61:34-41, 2020. © 2019 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Robert H Heflich
- U.S. Food and Drug Administration, National Center for Toxicological Research, Jefferson, Arkansas
| | | | - Andreas Zeller
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Francesco Marchetti
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Canada
| | - George R Douglas
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Canada
| | - Kristine L Witt
- National Institutes of Health, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | | | - Paul A White
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Canada
| |
Collapse
|
293
|
Rapani A, Nikiforaki D, Karagkouni D, Sfakianoudis K, Tsioulou P, Grigoriadis S, Maziotis E, Pantou A, Voutsina A, Pantou A, Koutsilieris M, Hatzigeorgiou A, Pantos K, Simopoulou M. Reporting on the Role of miRNAs and Affected Pathways on the Molecular Backbone of Ovarian Insufficiency: A Systematic Review and Critical Analysis Mapping of Future Research. Front Cell Dev Biol 2020; 8:590106. [PMID: 33511114 PMCID: PMC7835544 DOI: 10.3389/fcell.2020.590106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/30/2020] [Indexed: 12/19/2022] Open
Abstract
Ovarian insufficiency is identified as a perplexing entity in the long list of pathologies impairing fertility dynamics. The three distinct classifications of ovarian insufficiency are poor ovarian response, premature ovarian insufficiency/failure, and advanced maternal age, sharing the common denominator of deteriorated ovarian reserve. Despite efforts to define clear lines among the three, the vast heterogeneity and overlap of clinical characteristics renders their diagnosis and management challenging. Lack of a consensus has prompted an empirically based management coupled by uncertainty from the clinicians' perspective. Profiling of patients in the era of precision medicine seems to be the way forward, while the necessity for a novel approach is underlined. Implicating miRNAs in the quest for patient profiling is promising in light of their fundamental role in cellular and gene expression regulation. To this end, the current study sets out to explore and compare the three pathophysiologies-from a molecular point of view-in order to enable profiling of patients in the context of in vitro fertilization treatment and enrich the data required to practice individualized medicine. Following a systematic investigation of literature, data referring to miRNAs were collected for each patient category based on five included studies. miRNA-target pairs were retrieved from the DIANA-TarBase repository and microT-CDS. Gene and miRNA annotations were derived from Ensembl and miRbase. A subsequent gene-set enrichment analysis of miRNA targets was performed for each category separately. A literature review on the most crucial of the detected pathways was performed to reveal their relevance to fertility deterioration. Results supported that all three pathophysiologies share a common ground regarding the affected pathways, naturally attributed to the common denominator of ovarian insufficiency. As evidenced, miRNAs could be employed to explore the fine lines and diverse nature of pathophysiology since they constitute invaluable biomarkers. Interestingly, it is the differentiation through miRNAs and not through the molecular affected pathways that corresponds to the three distinctive categories. Alarming discrepancies among publications were revealed, pertaining to employment of empirical and arbitrary criteria in categorizing the patients. Following bioinformatic analysis, the final step of the current study consisted of a critical analysis of the molecular data sourced, providing a clear and unique insight into the physiological mechanisms involved. It is our intention to contribute to mapping future research dedicated to ovarian insufficiency and to help researchers navigate the overwhelming information published in molecular studies.
Collapse
Affiliation(s)
- Anna Rapani
- Department of Physiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
- Assisted Conception Unit, 2nd Department of Obstetrics and Gynecology, Aretaieion Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Dimitra Nikiforaki
- Department of Physiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Dimitra Karagkouni
- DIANA-Lab, Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
- Hellenic Pasteur Institute, Athens, Greece
| | | | - Petroula Tsioulou
- Department of Physiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
- Assisted Conception Unit, 2nd Department of Obstetrics and Gynecology, Aretaieion Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Sokratis Grigoriadis
- Department of Physiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
- Assisted Conception Unit, 2nd Department of Obstetrics and Gynecology, Aretaieion Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Evangelos Maziotis
- Department of Physiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
- Assisted Conception Unit, 2nd Department of Obstetrics and Gynecology, Aretaieion Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Amelia Pantou
- Centre for Human Reproduction, Genesis Athens Clinic, Athens, Greece
| | | | - Agni Pantou
- Centre for Human Reproduction, Genesis Athens Clinic, Athens, Greece
| | - Michael Koutsilieris
- Department of Physiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Artemis Hatzigeorgiou
- DIANA-Lab, Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
- Hellenic Pasteur Institute, Athens, Greece
| | | | - Mara Simopoulou
- Department of Physiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
- Assisted Conception Unit, 2nd Department of Obstetrics and Gynecology, Aretaieion Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
- *Correspondence: Mara Simopoulou,
| |
Collapse
|
294
|
Abstract
Recently, investigators have shown that only a few driver gene mutational events appear to be needed for cancer to occur. However, the reason that some mutational events precede others in the same cancer and the explanation for tissue-specific differences in this timing, remain mysterious. We here combine mathematical modeling with epidemiologic studies and sequencing data to address these questions. We suggest that the first driver event in cancers generally occurred at early ages and provide estimates for the fitness of different types of drivers during tumor evolution, showing how they vary with the tissue of origin. Cancer is driven by the sequential accumulation of genetic and epigenetic changes in oncogenes and tumor suppressor genes. The timing of these events is not well understood. Moreover, it is currently unknown why the same driver gene change appears as an early event in some cancer types and as a later event, or not at all, in others. These questions have become even more topical with the recent progress brought by genome-wide sequencing studies of cancer. Focusing on mutational events, we provide a mathematical model of the full process of tumor evolution that includes different types of fitness advantages for driver genes and carrying-capacity considerations. The model is able to recapitulate a substantial proportion of the observed cancer incidence in several cancer types (colorectal, pancreatic, and leukemia) and inherited conditions (Lynch and familial adenomatous polyposis), by changing only 2 tissue-specific parameters: the number of stem cells in a tissue and its cell division frequency. The model sheds light on the evolutionary dynamics of cancer by suggesting a generalized early onset of tumorigenesis followed by slow mutational waves, in contrast to previous conclusions. Formulas and estimates are provided for the fitness increases induced by driver mutations, often much larger than previously described, and highly tissue dependent. Our results suggest a mechanistic explanation for why the selective fitness advantage introduced by specific driver genes is tissue dependent.
Collapse
|
295
|
García-Nieto PE, Morrison AJ, Fraser HB. The somatic mutation landscape of the human body. Genome Biol 2019; 20:298. [PMID: 31874648 PMCID: PMC6930685 DOI: 10.1186/s13059-019-1919-5] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 12/10/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Somatic mutations in healthy tissues contribute to aging, neurodegeneration, and cancer initiation, yet they remain largely uncharacterized. RESULTS To gain a better understanding of the genome-wide distribution and functional impact of somatic mutations, we leverage the genomic information contained in the transcriptome to uniformly call somatic mutations from over 7500 tissue samples, representing 36 distinct tissues. This catalog, containing over 280,000 mutations, reveals a wide diversity of tissue-specific mutation profiles associated with gene expression levels and chromatin states. For example, lung samples with low expression of the mismatch-repair gene MLH1 show a mutation signature of deficient mismatch repair. In addition, we find pervasive negative selection acting on missense and nonsense mutations, except for mutations previously observed in cancer samples, which are under positive selection and are highly enriched in many healthy tissues. CONCLUSIONS These findings reveal fundamental patterns of tissue-specific somatic evolution and shed light on aging and the earliest stages of tumorigenesis.
Collapse
Affiliation(s)
- Pablo E García-Nieto
- Department of Biology, Stanford University, 371 Jane Stanford Way, Stanford, CA, 94305, USA
| | - Ashby J Morrison
- Department of Biology, Stanford University, 371 Jane Stanford Way, Stanford, CA, 94305, USA
| | - Hunter B Fraser
- Department of Biology, Stanford University, 371 Jane Stanford Way, Stanford, CA, 94305, USA.
| |
Collapse
|
296
|
Inoue S, Hirota Y, Ueno T, Fukui Y, Yoshida E, Hayashi T, Kojima S, Takeyama R, Hashimoto T, Kiyono T, Ikemura M, Taguchi A, Tanaka T, Tanaka Y, Sakata S, Takeuchi K, Muraoka A, Osuka S, Saito T, Oda K, Osuga Y, Terao Y, Kawazu M, Mano H. Uterine adenomyosis is an oligoclonal disorder associated with KRAS mutations. Nat Commun 2019; 10:5785. [PMID: 31857578 PMCID: PMC6923389 DOI: 10.1038/s41467-019-13708-y] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 11/21/2019] [Indexed: 01/26/2023] Open
Abstract
Uterine adenomyosis is a benign disorder that often co-occurs with endometriosis and/or leiomyoma, and impairs quality of life. The genomic features of adenomyosis are unknown. Here we apply next-generation sequencing to adenomyosis (70 individuals and 192 multi-regional samples), as well as co-occurring leiomyoma and endometriosis, and find recurring KRAS mutations in 26/70 (37.1%) of adenomyosis cases. Multi-regional sequencing reveals oligoclonality in adenomyosis, with some mutations also detected in normal endometrium and/or co-occurring endometriosis. KRAS mutations are more frequent in cases of adenomyosis with co-occurring endometriosis, low progesterone receptor (PR) expression, or progestin (dienogest; DNG) pretreatment. DNG's anti-proliferative effect is diminished via epigenetic silencing of PR in immortalized cells with mutant KRAS. Our genomic analyses suggest that adenomyotic lesions frequently contain KRAS mutations that may reduce DNG efficacy, and that adenomyosis and endometriosis may share molecular etiology, explaining their co-occurrence. These findings could lead to genetically guided therapy and/or relapse risk assessment after uterine-sparing surgery.
Collapse
Affiliation(s)
- Satoshi Inoue
- Department of Medical Genomics, The University of Tokyo, Tokyo, 113-0033, Japan.
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, 104-0045, Japan.
| | - Yasushi Hirota
- Department of Obstetrics and Gynecology, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Toshihide Ueno
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, 104-0045, Japan
| | - Yamato Fukui
- Department of Obstetrics and Gynecology, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Emiko Yoshida
- Department of Obstetrics and Gynecology, Juntendo University Faculty of Medicine, Tokyo, 113-8421, Japan
| | - Takuo Hayashi
- Department of Human Pathology, Juntendo University Faculty of Medicine, Tokyo, 113-8421, Japan
| | - Shinya Kojima
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, 104-0045, Japan
| | - Reina Takeyama
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, 104-0045, Japan
| | - Taiki Hashimoto
- Division of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, 104-0045, Japan
| | - Tohru Kiyono
- Division of Carcinogenesis and Cancer Prevention, and Department of Cell Culture Technology, National Cancer Center Research Institute, Tokyo, 104-0045, Japan
| | - Masako Ikemura
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Ayumi Taguchi
- Department of Obstetrics and Gynecology, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Tomoki Tanaka
- Department of Obstetrics and Gynecology, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Yosuke Tanaka
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, 104-0045, Japan
| | - Seiji Sakata
- Pathology Project for Molecular Targets, The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, 135-8550, Japan
| | - Kengo Takeuchi
- Pathology Project for Molecular Targets, The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, 135-8550, Japan
- Clinical Pathology Center, The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, 135-8550, Japan
- Division of Pathology, The Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, 135-8550, Japan
| | - Ayako Muraoka
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Satoko Osuka
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Tsuyoshi Saito
- Department of Human Pathology, Juntendo University Faculty of Medicine, Tokyo, 113-8421, Japan
| | - Katsutoshi Oda
- Department of Obstetrics and Gynecology, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Yutaka Osuga
- Department of Obstetrics and Gynecology, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Yasuhisa Terao
- Department of Obstetrics and Gynecology, Juntendo University Faculty of Medicine, Tokyo, 113-8421, Japan
| | - Masahito Kawazu
- Department of Medical Genomics, The University of Tokyo, Tokyo, 113-0033, Japan
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, 104-0045, Japan
| | - Hiroyuki Mano
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, 104-0045, Japan
| |
Collapse
|
297
|
Franco I, Helgadottir HT, Moggio A, Larsson M, Vrtačnik P, Johansson A, Norgren N, Lundin P, Mas-Ponte D, Nordström J, Lundgren T, Stenvinkel P, Wennberg L, Supek F, Eriksson M. Whole genome DNA sequencing provides an atlas of somatic mutagenesis in healthy human cells and identifies a tumor-prone cell type. Genome Biol 2019; 20:285. [PMID: 31849330 PMCID: PMC6918713 DOI: 10.1186/s13059-019-1892-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 11/18/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The lifelong accumulation of somatic mutations underlies age-related phenotypes and cancer. Mutagenic forces are thought to shape the genome of aging cells in a tissue-specific way. Whole genome analyses of somatic mutation patterns, based on both types and genomic distribution of variants, can shed light on specific processes active in different human tissues and their effect on the transition to cancer. RESULTS To analyze somatic mutation patterns, we compile a comprehensive genetic atlas of somatic mutations in healthy human cells. High-confidence variants are obtained from newly generated and publicly available whole genome DNA sequencing data from single non-cancer cells, clonally expanded in vitro. To enable a well-controlled comparison of different cell types, we obtain single genome data (92% mean coverage) from multi-organ biopsies from the same donors. These data show multiple cell types that are protected from mutagens and display a stereotyped mutation profile, despite their origin from different tissues. Conversely, the same tissue harbors cells with distinct mutation profiles associated to different differentiation states. Analyses of mutation rate in the coding and non-coding portions of the genome identify a cell type bearing a unique mutation pattern characterized by mutation enrichment in active chromatin, regulatory, and transcribed regions. CONCLUSIONS Our analysis of normal cells from healthy donors identifies a somatic mutation landscape that enhances the risk of tumor transformation in a specific cell population from the kidney proximal tubule. This unique pattern is characterized by high rate of mutation accumulation during adult life and specific targeting of expressed genes and regulatory regions.
Collapse
Affiliation(s)
- Irene Franco
- Department of Biosciences and Nutrition, Center for Innovative Medicine, Karolinska Institutet, Huddinge, Sweden.
| | - Hafdis T Helgadottir
- Department of Biosciences and Nutrition, Center for Innovative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Aldo Moggio
- Department of Medicine Huddinge, Integrated Cardio Metabolic Center, Karolinska Institutet, Huddinge, Sweden
| | - Malin Larsson
- Science for Life Laboratory, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Peter Vrtačnik
- Department of Biosciences and Nutrition, Center for Innovative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Anna Johansson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Nina Norgren
- Science for Life Laboratory, Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Pär Lundin
- Department of Biosciences and Nutrition, Center for Innovative Medicine, Karolinska Institutet, Huddinge, Sweden
- Science for Life Laboratory, Department of Biochemistry and Biophysics (DBB), Stockholm University, Stockholm, Sweden
| | - David Mas-Ponte
- Genome Data Science, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
| | - Johan Nordström
- Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet, Division of Transplantation Surgery, Karolinska University Hospital, Huddinge, Sweden
| | - Torbjörn Lundgren
- Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet, Division of Transplantation Surgery, Karolinska University Hospital, Huddinge, Sweden
| | - Peter Stenvinkel
- Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet, Division of Renal Medicine, Karolinska University Hospital, Huddinge, Sweden
| | - Lars Wennberg
- Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet, Division of Transplantation Surgery, Karolinska University Hospital, Huddinge, Sweden
| | - Fran Supek
- Genome Data Science, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Maria Eriksson
- Department of Biosciences and Nutrition, Center for Innovative Medicine, Karolinska Institutet, Huddinge, Sweden.
| |
Collapse
|
298
|
Steensma DP, Ebert BL. Clonal hematopoiesis as a model for premalignant changes during aging. Exp Hematol 2019; 83:48-56. [PMID: 31838005 DOI: 10.1016/j.exphem.2019.12.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 12/06/2019] [Accepted: 12/07/2019] [Indexed: 12/30/2022]
Abstract
Over the course of the human life span, somatic DNA mutations accumulate in healthy tissues. This process has been most clearly described in blood and bone marrow, esophagus, colon, and skin, but cumulative DNA damage likely affects all tissues of the body. Although most acquired genetic variants have no discernable functional consequences, some randomly occurring somatic mutations confer a relative fitness advantage on a single stem cell and its progeny compared with surrounding cells, which may lead to progressive expansion of a clone (i.e., a genetically identical group of cells). When these mutations occur in a cell with the capacity to self-renew and expand, the mutations persist, and such clonal expansion is a risk factor for further mutation acquisition and clonal evolution. Hematopoietic stem cells are a special case of clonal expansion because both the stem cells and their blood cell progeny circulate in large numbers, and these cells are not subject to some of the anatomical restrictions that characterize other tissues in which somatic mutations conferring a fitness advantage also occur. Therefore, clonally restricted hematopoiesis can have biological and clinical consequences that are distinct from clonal expansions in other tissues. Such consequences include not only clonal progression to overt myeloid neoplasia (or, less commonly, to lymphoid neoplasia) driven by acquisition of secondary mutations in the cells of the expanded clone, but also cardiovascular events and, most likely, other diseases that are influenced by aberrant function of mutant blood cells. A more detailed understanding of how clonal hematopoiesis arises and how clonal selection and expansion occur, as well as development of strategies to avert the clinical consequences associated with clonal hematopoiesis, may both improve public health and yield more general insights into the biology of aging.
Collapse
Affiliation(s)
- David P Steensma
- Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA.
| | - Benjamin L Ebert
- Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA
| |
Collapse
|
299
|
Krimmel-Morrison JD, Ghezelayagh TS, Lian S, Zhang Y, Fredrickson J, Nachmanson D, Baker KT, Radke MR, Hun E, Norquist BM, Emond MJ, Swisher EM, Risques RA. Characterization of TP53 mutations in Pap test DNA of women with and without serous ovarian carcinoma. Gynecol Oncol 2019; 156:407-414. [PMID: 31839337 DOI: 10.1016/j.ygyno.2019.11.124] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 11/28/2019] [Accepted: 11/30/2019] [Indexed: 02/06/2023]
Abstract
OBJECTIVE Pap tests hold promise as a molecular diagnostic for serous ovarian cancer, but previous studies reported limited sensitivity. Furthermore, the presence of somatic mutations in normal tissue is increasingly recognized as a challenge to the specificity of mutation-based cancer diagnostics. We applied an ultra-deep sequencing method with the goal of improving sensitivity and characterizing the landscape of low-frequency somatic TP53 mutations in Pap tests. METHODS We used CRISPR-DS to deeply sequence (mean Duplex depth ~3000×) the TP53 gene in 30 Pap tests from 21 women without cancer and 9 women with serous ovarian carcinoma with known TP53 driver mutations. Mutations were annotated and compared to those in the TP53 cancer database. RESULTS The tumor-derived mutation was identified in 3 of 8 Pap tests from women with ovarian cancer and intact tubes. In addition, 221 low-frequency (≲0.001) exonic TP53 mutations were identified in Pap tests from women with ovarian cancer (94 mutations) and without ovarian cancer (127 mutations). Many of these mutations resembled TP53 mutations found in cancer: they impaired protein activity, were predicted to be pathogenic, and clustered in exons 5 to 8 and hotspot codons. Cancer-like mutations were identified in all women but at higher frequency in women with ovarian cancer. CONCLUSIONS Pap tests have low sensitivity for ovarian cancer detection and carry abundant low-frequency TP53 mutations. These mutations are more frequently pathogenic in women with ovarian cancer. Determining whether low-frequency TP53 mutations in normal gynecologic tissues are associated with an increased cancer risk warrants further study.
Collapse
Affiliation(s)
- Jeffrey D Krimmel-Morrison
- Department of Medicine, University of Washington, Seattle, WA 98195, USA; Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Talayeh S Ghezelayagh
- Department of Pathology, University of Washington, Seattle, WA 98195, USA; Department of Obstetrics and Gynecology, University of Washington, Seattle, WA 98195, USA
| | - Shenyi Lian
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Yuezheng Zhang
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Jeanne Fredrickson
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Daniela Nachmanson
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Kathryn T Baker
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Marc R Radke
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA 98195, USA
| | - Enna Hun
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA 98195, USA
| | - Barbara M Norquist
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA 98195, USA
| | - Mary J Emond
- Department of Statistics, University of Washington, Seattle, WA 98195, USA
| | - Elizabeth M Swisher
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA 98195, USA
| | - Rosa Ana Risques
- Department of Pathology, University of Washington, Seattle, WA 98195, USA.
| |
Collapse
|
300
|
Evans JJ, Alkaisi MM, Sykes PH. Tumour Initiation: a Discussion on Evidence for a "Load-Trigger" Mechanism. Cell Biochem Biophys 2019; 77:293-308. [PMID: 31598831 PMCID: PMC6841748 DOI: 10.1007/s12013-019-00888-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 09/23/2019] [Indexed: 12/18/2022]
Abstract
Appropriate mechanical forces on cells are vital for normal cell behaviour and this review discusses the possibility that tumour initiation depends partly on the disruption of the normal physical architecture of the extracellular matrix (ECM) around a cell. The alterations that occur thence promote oncogene expression. Some questions, that are not answered with certainty by current consensus mechanisms of tumourigenesis, are elegantly explained by the triggering of tumours being a property of the physical characteristics of the ECM, which is operative following loading of the tumour initiation process with a relevant gene variant. Clinical observations are consistent with this alternative hypothesis which is derived from studies that have, together, accumulated an extensive variety of data incorporating biochemical, genetic and clinical findings. Thus, this review provides support for the view that the ECM may have an executive function in induction of a tumour. Overall, reported observations suggest that either restoring an ECM associated with homeostasis or targeting the related signal transduction mechanisms may possibly be utilised to modify or control the early progression of cancers. The review provides a coherent template for discussing the notion, in the context of contemporary knowledge, that tumourigenesis is an alliance of biochemistry, genetics and biophysics, in which the physical architecture of the ECM may be a fundamental component. For more definitive clarification of the concept there needs to be a phalanx of experiments conceived around direct questions that are raised by this paper.
Collapse
Affiliation(s)
- John J Evans
- Department of Obstetrics and Gynaecology, University of Otago Christchurch, Christchurch, New Zealand.
- MacDiarmid Institute of Advanced Materials and Nanotechnology, Christchurch, New Zealand.
| | - Maan M Alkaisi
- MacDiarmid Institute of Advanced Materials and Nanotechnology, Christchurch, New Zealand
- Department of Electrical and Computer Engineering, University of Canterbury, Christchurch, New Zealand
| | - Peter H Sykes
- Department of Obstetrics and Gynaecology, University of Otago Christchurch, Christchurch, New Zealand
| |
Collapse
|