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Kundranda MN, Kemkes AC, Evans MC, Flannery CA, Hall DW, Hoag JR, Therala N, Thakkar SG, De La O JP. Associations with other cancer-related biomarkers might contribute to poor outcomes in RAS-altered, younger patients with colorectal cancer. Oncologist 2024:oyae153. [PMID: 38886182 DOI: 10.1093/oncolo/oyae153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 05/24/2024] [Indexed: 06/20/2024] Open
Abstract
Colorectal cancer (CRC) is a common cancer in younger adults. In patients undergoing liver resection with RAS-altered CRCs, there is evidence suggesting younger patients have worse outcomes than older patients. To explain this pattern, differences in associations between RAS status and other cancer-related biomarkers in tumors from younger versus older patients with CRC were evaluated in a cohort of 925 patients with CRC, 277 (30.0%) of whom were ≤50 years old, and 454 (49.1%) who had RAS-altered tumors. For 3 biomarkers, RNF43, APC, and microsatellite instability (MSI), the association with RAS status was significantly modified by age after adjustment for multiple testing. Specifically, younger patients with RAS-altered tumors were more likely to be MSI-high, RNF43 mutated, and APC wild type. These differences might contribute to the observed pattern of diminished survival in younger versus older patients with CRC with RAS-mutated tumors undergoing liver metastasis resection.
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Affiliation(s)
| | | | - Mark C Evans
- Exact Sciences Corporation, Madison, WI, United States
| | | | - David W Hall
- Exact Sciences Corporation, Madison, WI, United States
| | - Jess R Hoag
- Exact Sciences Corporation, Madison, WI, United States
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2
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Tam YB, Low K, Ps H, Chadha M, Burns J, Wilding CP, Arthur A, Chen TW, Thway K, Sadanandam A, Jones RL, Huang PH. Proteomic features of soft tissue tumours in adolescents and young adults. COMMUNICATIONS MEDICINE 2024; 4:93. [PMID: 38762630 PMCID: PMC11102500 DOI: 10.1038/s43856-024-00522-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 05/07/2024] [Indexed: 05/20/2024] Open
Abstract
BACKGROUND Adolescents and young adult (AYA) patients with soft tissue tumours including sarcomas are an underserved group with disparities in treatment outcomes. METHODS To define the molecular features between AYA and older adult (OA) patients, we analysed the proteomic profiles of a large cohort of soft tissue tumours across 10 histological subtypes (AYA n = 66, OA n = 243), and also analysed publicly available functional genomic data from soft tissue tumour cell lines (AYA n = 5, OA n = 8). RESULTS Biological hallmarks analysis demonstrates that OA tumours are significantly enriched in MYC targets compared to AYA tumours. By comparing the patient-level proteomic data with functional genomic profiles from sarcoma cell lines, we show that the mRNA splicing pathway is an intrinsic vulnerability in cell lines from OA patients and that components of the spliceosome complex are independent prognostic factors for metastasis free survival in AYA patients. CONCLUSIONS Our study highlights the importance of performing age-specific molecular profiling studies to identify risk stratification tools and targeted agents tailored for the clinical management of AYA patients.
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Affiliation(s)
- Yuen Bun Tam
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - Kaan Low
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - Hari Ps
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - Madhumeeta Chadha
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - Jessica Burns
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - Christopher P Wilding
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - Amani Arthur
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - Tom W Chen
- Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan
- Graduate Institute of Oncology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Khin Thway
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Anguraj Sadanandam
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - Robin L Jones
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
- Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
| | - Paul H Huang
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom.
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Zhou Y, Chen X, Chen J, Kendrick CD, Ramanathan RK, Graham RP, Kossick KF, Boardman LA, Barrett MT. Genomic landscape of diploid and aneuploid microsatellite stable early onset colorectal cancer. Sci Rep 2024; 14:9368. [PMID: 38654044 DOI: 10.1038/s41598-024-59398-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 04/10/2024] [Indexed: 04/25/2024] Open
Abstract
Although colorectal cancer (CRC) remains the second leading cause of cancer-related death in the United States, the overall incidence and mortality from the disease have declined in recent decades. In contrast, there has been a steady increase in the incidence of CRC in individuals under 50 years of age. Hereditary syndromes contribute disproportionately to early onset CRC (EOCRC). These include microsatellite instability high (MSI+) tumors arising in patients with Lynch Syndrome. However, most EOCRCs are not associated with familial syndromes or MSI+ genotypes. Comprehensive genomic profiling has provided the basis of improved more personalized treatments for older CRC patients. However, less is known about the basis of sporadic EOCRC. To define the genomic landscape of EOCRC we used DNA content flow sorting to isolate diploid and aneuploid tumor fractions from 21 non-hereditary cases. We then generated whole exome mutational profiles for each case and whole genome copy number, telomere length, and EGFR immunohistochemistry (IHC) analyses on subsets of samples. These results discriminate the molecular features of diploid and aneuploid EOCRC and provide a basis for larger population-based studies and the development of effective strategies to monitor and treat this emerging disease.
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Affiliation(s)
- Yumei Zhou
- Department of Research, Mayo Clinic in Arizona, Scottsdale, AZ, USA
| | - Xianfeng Chen
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, 55905, USA
| | - Jun Chen
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, 55905, USA
| | - Conner D Kendrick
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Ramesh K Ramanathan
- Mayo Clinic Cancer Center, Phoenix, AZ, 85054, USA
- Ironwood Cancer and Research Center, Scottsdale, AZ, 85260, USA
| | | | - Kimberlee F Kossick
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Lisa A Boardman
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Michael T Barrett
- Department of Research, Mayo Clinic in Arizona, Scottsdale, AZ, USA.
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic in Arizona, Scottsdale, AZ, USA.
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4
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Zhao X, Fan X, Lin X, Guo B, Yu Y. Deciphering age-specific molecular features in cervical cancer and constructing an angio-immune prognostic model. Medicine (Baltimore) 2024; 103:e37717. [PMID: 38608077 PMCID: PMC11018232 DOI: 10.1097/md.0000000000037717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 03/04/2024] [Indexed: 04/14/2024] Open
Abstract
Cancer incidence is increasingly seen in younger individuals. Molecular distinctions between young and elderly patients at onset are understudied. This study used public databases to explore genomic, transcriptomic, and immune-related features across age groups in cervical cancer. Additionally, it aims to create a prognostic model applicable across diverse age cohorts, enabling precise patient stratification, and personalized therapies. Gene mutations, expression data, and clinicopathological information were obtained from 317 cervical cancer patients. These patients were divided into a young group and an old group based on the median age of onset. The characteristics of differential gene mutation, gene expression, and immune cells analysis were analyzed by R software. Finally, the prognostic model was constructed by univariate Cox, least absolute shrinkage and selection operator, and multivariate Cox regression analyses of angiogenic and immune gene sets. Its validity was further confirmed using an additional 300 cervical squamous cell carcinoma and endocervical adenocarcinoma tissues. Cervical cancer patients at elderly onset age exhibit a significantly higher frequency of NOTCH1 and TP53 driver mutations compared to young patients, along with a notably higher tumor mutational burden. However, there were no significant differences between the 2 groups in terms of genomic instability and age-related mutational signatures. Differential gene expression analysis revealed that the young group significantly upregulated interferon-alpha and gamma responses and exhibited significantly higher activity in multiple metabolic pathways. Immune microenvironment analysis indicated enrichment of dendritic cells and natural killer cells in the young group, while transforming growth factor-β signature was enriched in the elderly group, indicating a higher degree of immune exclusion. A multigene prognostic model based on angiogenesis and T cell immune gene sets showed excellent prognostic performance independent of clinical factors such as age. High-risk groups identified by the model exhibit significant activation of tumor-promoting processes, such as metastasis and angiogenesis. Our study reveals distinct patterns in cancer-driving mechanisms, biological processes, and immune system status between young and elderly patients at onset with cervical cancer. These findings shed light on the age-specific underlying mechanisms of carcinogenesis. Furthermore, an independent molecular prognostic model is constructed to provide valuable references for patient stratification and the development of potential drug targets.
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Affiliation(s)
- Xin Zhao
- Department of Public Health, International College, Krirk University, Bangkok, Thailand
| | - Xichen Fan
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xiu Lin
- Department of Public Health, International College, Krirk University, Bangkok, Thailand
| | - Baozhu Guo
- Department of Public Health, International College, Krirk University, Bangkok, Thailand
| | - Yanqin Yu
- Department of Public Health, International College, Krirk University, Bangkok, Thailand
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Al-Danakh A, Safi M, Jian Y, Yang L, Zhu X, Chen Q, Yang K, Wang S, Zhang J, Yang D. Aging-related biomarker discovery in the era of immune checkpoint inhibitors for cancer patients. Front Immunol 2024; 15:1348189. [PMID: 38590525 PMCID: PMC11000233 DOI: 10.3389/fimmu.2024.1348189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 01/29/2024] [Indexed: 04/10/2024] Open
Abstract
Older patients with cancer, particularly those over 75 years of age, often experience poorer clinical outcomes compared to younger patients. This can be attributed to age-related comorbidities, weakened immune function, and reduced tolerance to treatment-related adverse effects. In the immune checkpoint inhibitors (ICI) era, age has emerged as an influential factor impacting the discovery of predictive biomarkers for ICI treatment. These age-linked changes in the immune system can influence the composition and functionality of tumor-infiltrating immune cells (TIICs) that play a crucial role in the cancer response. Older patients may have lower levels of TIICs infiltration due to age-related immune senescence particularly T cell function, which can limit the effectivity of cancer immunotherapies. Furthermore, age-related immune dysregulation increases the exhaustion of immune cells, characterized by the dysregulation of ICI-related biomarkers and a dampened response to ICI. Our review aims to provide a comprehensive understanding of the mechanisms that contribute to the impact of age on ICI-related biomarkers and ICI response. Understanding these mechanisms will facilitate the development of treatment approaches tailored to elderly individuals with cancer.
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Affiliation(s)
- Abdullah Al-Danakh
- Department of Urology, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Mohammed Safi
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Yuli Jian
- Department of Biochemistry and Molecular Biology, Institute of Glycobiology, Dalian Medical University, Dalian, China
| | - Linlin Yang
- Department of Urology, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Xinqing Zhu
- Department of Urology, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Qiwei Chen
- Department of Urology, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Kangkang Yang
- Institute for Genome Engineered Animal Models of Human Diseases, National Center of Genetically Engineered Animal Models for International Research, Dalian Medical University, Dalian, Liaoning, China
| | - Shujing Wang
- Department of Biochemistry and Molecular Biology, Institute of Glycobiology, Dalian Medical University, Dalian, China
| | - Jianjun Zhang
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Deyong Yang
- Department of Urology, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
- Department of Surgery, Healinghands Clinic, Dalian, Liaoning, China
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Ribelles N, Pascual J, Galvez-Carvajal L, Ruiz-Medina S, Garcia-Corbacho J, Benitez JC, Dominguez-Recio ME, Torres E, Oliva L, Zalabardo M, Rueda A, Alba E. Increasing Annual Cancer Incidence in Patients Age 20-49 Years: A Real-Data Study. JCO Glob Oncol 2024; 10:e2300363. [PMID: 38513186 DOI: 10.1200/go.23.00363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/05/2024] [Accepted: 02/05/2024] [Indexed: 03/23/2024] Open
Abstract
PURPOSE Data from population-based studies have shown an increased incidence of certain types of neoplasms in patients younger than 50 years (early-onset cancer [EOC]); however, little information is derived from other real-world data sources. In a nonpopulation registry, we analyzed changes in the incidence of several neoplasms in successive generations. METHODS This cross-sectional study included all patients with a cancer diagnosis registered in one university hospital in Málaga, Spain, between 1998 and 2021, and 18 neoplasms were analyzed. For each neoplasm, the proportion of patients younger than 50 years and age 50 years and older (late-onset cancer [LOC]) of the total number of patients diagnosed each year was determined. In addition, the age limit was lowered to 45-40 years. Changes in these proportions between each year and the following year were assessed by calculating the annual percentage change (APC), and a final assessment of these changes was performed by determining the average APC (AAPC). RESULTS Of the 24,596 patients, 5,466 (22.2%) had EOC, and 19,130 (77.8%) had LOC. The incidence of all tumors increased throughout the study period in both age groups. The AAPC increase was higher in patients with EOC than in those with LOC for the following neoplasms: head and neck (6.1% v 4.6%), colon (11.0% v 8.2%), testicular (16.3% v -13.1%), non-Hodgkin lymphoma (8.4% v 5.9%), rectum (16.1% v 6.8%), kidney (27.8% v 20.1%), and sarcoma (43.4% v 28.6%). This increase was confirmed in patients younger than 45 years and 40 years. CONCLUSION Our results are consistent with the data published for most tumor sites analyzed. This global public health problem requires the utmost attention to decrease excess cancer in young patients.
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Affiliation(s)
- Nuria Ribelles
- Medical Oncology Intercenter Unit, Regional and Virgen de la Victoria University Hospitals, IBIMA, Malaga, Spain
| | - Javier Pascual
- Medical Oncology Intercenter Unit, Regional and Virgen de la Victoria University Hospitals, IBIMA, Malaga, Spain
- Oncology Biomedical Research National Network (CIBERONC-ISCIII), Madrid, Spain
| | - Laura Galvez-Carvajal
- Medical Oncology Intercenter Unit, Regional and Virgen de la Victoria University Hospitals, IBIMA, Malaga, Spain
| | - Sofía Ruiz-Medina
- Medical Oncology Intercenter Unit, Regional and Virgen de la Victoria University Hospitals, IBIMA, Malaga, Spain
| | - Javier Garcia-Corbacho
- Medical Oncology Intercenter Unit, Regional and Virgen de la Victoria University Hospitals, IBIMA, Malaga, Spain
| | - Jose Carlos Benitez
- Medical Oncology Intercenter Unit, Regional and Virgen de la Victoria University Hospitals, IBIMA, Malaga, Spain
| | - Maria Emilia Dominguez-Recio
- Medical Oncology Intercenter Unit, Regional and Virgen de la Victoria University Hospitals, IBIMA, Malaga, Spain
| | - Esperanza Torres
- Medical Oncology Intercenter Unit, Regional and Virgen de la Victoria University Hospitals, IBIMA, Malaga, Spain
| | - Lucia Oliva
- Medical Oncology Intercenter Unit, Regional and Virgen de la Victoria University Hospitals, IBIMA, Malaga, Spain
| | - Manuel Zalabardo
- Medical Oncology Intercenter Unit, Regional and Virgen de la Victoria University Hospitals, IBIMA, Malaga, Spain
| | - Antonio Rueda
- Medical Oncology Intercenter Unit, Regional and Virgen de la Victoria University Hospitals, IBIMA, Malaga, Spain
| | - Emilio Alba
- Medical Oncology Intercenter Unit, Regional and Virgen de la Victoria University Hospitals, IBIMA, Malaga, Spain
- Oncology Biomedical Research National Network (CIBERONC-ISCIII), Madrid, Spain
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Ontiveros CO, Murray CE, Crossland G, Curiel TJ. Considerations and Approaches for Cancer Immunotherapy in the Aging Host. Cancer Immunol Res 2023; 11:1449-1461. [PMID: 37769157 DOI: 10.1158/2326-6066.cir-23-0121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/16/2023] [Accepted: 08/22/2023] [Indexed: 09/30/2023]
Abstract
Advances in cancer immunotherapy are improving treatment successes in many distinct cancer types. Nonetheless, most tumors fail to respond. Age is the biggest risk for most cancers, and the median population age is rising worldwide. Advancing age is associated with manifold alterations in immune cell types, abundance, and functions, rather than simple declines in these metrics, the consequences of which remain incompletely defined. Our understanding of the effects of host age on immunotherapy mechanisms, efficacy, and adverse events remains incomplete. A deeper understanding of age effects in all these areas is required. Most cancer immunotherapy preclinical studies examine young subjects and fail to assess age contributions, a remarkable deficit given the known importance of age effects on immune cells and factors mediating cancer immune surveillance and immunotherapy efficacy. Notably, some cancer immunotherapies are more effective in aged versus young hosts, while others fail despite efficacy in the young. Here, we review our current understanding of age effects on immunity and associated nonimmune cells, the tumor microenvironment, cancer immunotherapy, and related adverse effects. We highlight important knowledge gaps and suggest areas for deeper enquiries, including in cancer immune surveillance, treatment response, adverse event outcomes, and their mitigation.
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Affiliation(s)
- Carlos O Ontiveros
- UT Health San Antonio Long School of Medicine and Graduate School of Biomedical Sciences, The University of Texas, San Antonio, Texas
| | - Clare E Murray
- UT Health San Antonio Long School of Medicine and Graduate School of Biomedical Sciences, The University of Texas, San Antonio, Texas
| | - Grace Crossland
- Graduate School of Microbiology and Immunology, Dartmouth College, Hanover, New Hampshire
- The Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, New Hampshire
| | - Tyler J Curiel
- UT Health San Antonio Long School of Medicine and Graduate School of Biomedical Sciences, The University of Texas, San Antonio, Texas
- Graduate School of Microbiology and Immunology, Dartmouth College, Hanover, New Hampshire
- The Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, New Hampshire
- Dartmouth Health and Dartmouth Cancer Center, Lebanon, New Hampshire
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8
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Dos Santos GA, Chatsirisupachai K, Avelar RA, de Magalhães JP. Transcriptomic analysis reveals a tissue-specific loss of identity during ageing and cancer. BMC Genomics 2023; 24:644. [PMID: 37884865 PMCID: PMC10604446 DOI: 10.1186/s12864-023-09756-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 10/20/2023] [Indexed: 10/28/2023] Open
Abstract
INTRODUCTION Understanding changes in cell identity in cancer and ageing is of great importance. In this work, we analyzed how gene expression changes in human tissues are associated with tissue specificity during cancer and ageing using transcriptome data from TCGA and GTEx. RESULTS We found significant downregulation of tissue-specific genes during ageing in 40% of the tissues analyzed, which suggests loss of tissue identity with age. For most cancer types, we have noted a consistent pattern of downregulation in genes that are specific to the tissue from which the tumor originated. Moreover, we observed in cancer an activation of genes not usually expressed in the tissue of origin as well as an upregulation of genes specific to other tissues. These patterns in cancer were associated with patient survival. The age of the patient, however, did not influence these patterns. CONCLUSION We identified loss of cellular identity in 40% of the tissues analysed during human ageing, and a clear pattern in cancer, where during tumorigenesis cells express genes specific to other organs while suppressing the expression of genes from their original tissue. The loss of cellular identity observed in cancer is associated with prognosis and is not influenced by age, suggesting that it is a crucial stage in carcinogenesis.
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Affiliation(s)
- Gabriel Arantes Dos Santos
- Laboratory of Medical Investigation (LIM55), Urology Department, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
- Genomics of Ageing and Rejuvenation Lab, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, B15 2WB, UK
| | - Kasit Chatsirisupachai
- Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, L7 8TX, UK
| | - Roberto A Avelar
- Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, L7 8TX, UK
| | - João Pedro de Magalhães
- Genomics of Ageing and Rejuvenation Lab, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, B15 2WB, UK.
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Ketteler A, Blumenthal DB. Demographic confounders distort inference of gene regulatory and gene co-expression networks in cancer. Brief Bioinform 2023; 24:bbad413. [PMID: 37985453 DOI: 10.1093/bib/bbad413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/19/2023] [Accepted: 10/26/2023] [Indexed: 11/22/2023] Open
Abstract
Gene regulatory networks (GRNs) and gene co-expression networks (GCNs) allow genome-wide exploration of molecular regulation patterns in health and disease. The standard approach for obtaining GRNs and GCNs is to infer them from gene expression data, using computational network inference methods. However, since network inference methods are usually applied on aggregate data, distortion of the networks by demographic confounders might remain undetected, especially because gene expression patterns are known to vary between different demographic groups. In this paper, we present a computational framework to systematically evaluate the influence of demographic confounders on network inference from gene expression data. Our framework compares similarities between networks inferred for different demographic groups with similarity distributions obtained for random splits of the expression data. Moreover, it allows to quantify to which extent demographic groups are represented by networks inferred from the aggregate data in a confounder-agnostic way. We apply our framework to test four widely used GRN and GCN inference methods as to their robustness w. r. t. confounding by age, ethnicity and sex in cancer. Our findings based on more than $ {44000}$ inferred networks indicate that age and sex confounders play an important role in network inference for certain cancer types, emphasizing the importance of incorporating an assessment of the effect of demographic confounders into network inference workflows. Our framework is available as a Python package on GitHub: https://github.com/bionetslab/grn-confounders.
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Affiliation(s)
- Anna Ketteler
- Biomedical Network Science Lab, Department Artificial Intelligence in Biomedical Engineering, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - David B Blumenthal
- Biomedical Network Science Lab, Department Artificial Intelligence in Biomedical Engineering, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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Lipsyc-Sharf M, Jain E, Collins LC, Rosenberg SM, Ruddy KJ, Tamimi RM, Schapira L, Come SE, Peppercorn JM, Borges VF, Warner E, Snow C, Krop IE, Kim D, Weiss J, Zanudo JGT, Partridge AH, Wagle N, Waks AG. Genomics of ERBB2-Positive Breast Cancer in Young Women Before and After Exposure to Chemotherapy Plus Trastuzumab. JCO Precis Oncol 2023; 7:e2300076. [PMID: 37364233 DOI: 10.1200/po.23.00076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/18/2023] [Accepted: 05/08/2023] [Indexed: 06/28/2023] Open
Abstract
PURPOSE Erb-B2 receptor tyrosine kinase 2 (ERBB2)-positive breast cancer (BC) is particularly common in young women. Genomic features of ERBB2-positive tumors before and after chemotherapy and trastuzumab (chemo + H) have not been described in young women and are important for guiding study of therapeutic resistance in this population. METHODS From a large prospective cohort of women age 40 years or younger with BC, we identified patients with ERBB2-positive BC and tumor tissue available before and after chemo + H. Whole-exome sequencing (WES) was performed on each tumor and on germline DNA from blood. Tumor-normal pairs were analyzed for mutations and copy number (CN) changes. RESULTS Twenty-two women had successful WES on samples from at least one time point; 12 of these had paired sequencing results from before and after chemo + H and 10 had successful sequencing from either time point. TP53 was the only significantly recurrently mutated gene in both pre- and post-treatment samples. MYC gene amplification was observed in four post-treatment tumors. Seven of 12 patients with paired samples showed acquired and/or clonally enriched alterations in cancer-related genes. One patient had an increased clonality putative activating mutation in ERBB2. Another patient acquired a clonal hotspot mutation in TP53. Other genomic changes acquired in post-treatment specimens included alterations in NOTCH2, STIL, PIK3CA, and GATA3. There was no significant change in median ERBB2 CN (20.3 v 22.6; Wilcoxon P = .79) between paired samples. CONCLUSION ERBB2-positive BCs in young women displayed substantial genomic evolution after treatment with chemo + H. Approximately half of patients with paired samples demonstrated acquired and/or clonally enriched genomic changes in cancer genes. ERBB2 CN changes were uncommon. We identified several genes warranting exploration as potential mechanisms of resistance to therapy in this population.
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Affiliation(s)
- Marla Lipsyc-Sharf
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA
- Harvard Medical School, Boston, MA
| | - Esha Jain
- Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
- Repare Therapeutics, Cambridge, MA
| | - Laura C Collins
- Harvard Medical School, Boston, MA
- Beth Israel Deaconess Medical Center, Boston, MA
| | | | | | - Rulla M Tamimi
- Weill Cornell Medicine, New York, NY
- Brigham and Women's Hospital, Boston, MA
| | | | - Steven E Come
- Harvard Medical School, Boston, MA
- Breast Medical Oncology Program, Beth Israel Deaconess Medical Center and Dana-Farber/Harvard Cancer Center, Boston, MA
| | | | | | - Ellen Warner
- Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Craig Snow
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA
| | - Ian E Krop
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA
- Yale Cancer Center, New Haven, CT
| | - Dewey Kim
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Jakob Weiss
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Jorge Gomez Tejeda Zanudo
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Ann H Partridge
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA
- Harvard Medical School, Boston, MA
| | - Nikhil Wagle
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA
- Harvard Medical School, Boston, MA
| | - Adrienne G Waks
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA
- Harvard Medical School, Boston, MA
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11
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Schuster ALR, Crossnohere NL, Bachini M, Blair CK, Carpten JD, Claus EB, Colditz GA, Ding L, Drake BF, Fields RC, Janeway KA, Kwan BM, Lenz HJ, Ma Q, Mishra SI, Paskett ED, Rebbeck TR, Ricker C, Stern MC, Sussman AL, Tiner JC, Trent JM, Verhaak RGW, Wagle N, Willman C, Bridges JFP. Priorities to Promote Participant Engagement in the Participant Engagement and Cancer Genome Sequencing (PE-CGS) Network. Cancer Epidemiol Biomarkers Prev 2023; 32:487-495. [PMID: 36791345 PMCID: PMC10068438 DOI: 10.1158/1055-9965.epi-22-0356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 11/21/2022] [Accepted: 02/07/2023] [Indexed: 02/17/2023] Open
Abstract
BACKGROUND Engaging diverse populations in cancer genomics research is of critical importance and is a fundamental goal of the NCI Participant Engagement and Cancer Genome Sequencing (PE-CGS) Network. Established as part of the Cancer Moonshot, PE-CGS is a consortium of stakeholders including clinicians, scientists, genetic counselors, and representatives of potential study participants and their communities. Participant engagement is an ongoing, bidirectional, and mutually beneficial interaction between study participants and researchers. PE-CGS sought to set priorities in participant engagement for conducting the network's research. METHODS PE-CGS deliberatively engaged its stakeholders in the following four-phase process to set the network's research priorities in participant engagement: (i) a brainstorming exercise to elicit potential priorities; (ii) a 2-day virtual meeting to discuss priorities; (iii) recommendations from the PE-CGS External Advisory Panel to refine priorities; and (iv) a virtual meeting to set priorities. RESULTS Nearly 150 PE-CGS stakeholders engaged in the process. Five priorities were set: (i) tailor education and communication materials for participants throughout the research process; (ii) identify measures of participant engagement; (iii) identify optimal participant engagement strategies; (iv) understand cancer disparities in the context of cancer genomics research; and (v) personalize the return of genomics findings to participants. CONCLUSIONS PE-CGS is pursuing these priorities to meaningfully engage diverse and underrepresented patients with cancer and posttreatment cancer survivors as participants in cancer genomics research and, subsequently, generate new discoveries. IMPACT Data from PE-CGS will be shared with the broader scientific community in a manner consistent with participant informed consent and community agreement.
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Affiliation(s)
- Anne LR. Schuster
- Department of Biomedical Informatics, The Ohio State University College of Medicine, Columbus, Ohio
| | - Norah L. Crossnohere
- Division of General Internal Medicine, Department of Internal Medicine, The Ohio State University, Columbus, Ohio
| | | | - Cindy K. Blair
- Department of Internal Medicine, University of New Mexico Comprehensive Cancer Center and Health Sciences Center, Albuquerque, New Mexico
| | - John D. Carpten
- Institute of Translational Genomics, Department of Translational Genomics, Keck School of Medicine USC, Norris Comprehensive Cancer Center, Los Angeles, California
| | - Elizabeth B. Claus
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut
- Department of Neurosurgery, Brigham and Women's Hospital, Boston, Massachusetts
| | - Graham A. Colditz
- Department of Surgery, Washington University School of Medicine, Alvin J. Siteman Cancer Center, St. Louis, Missouri
| | - Li Ding
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Bettina F. Drake
- Division of Public Health Sciences, Washington University School of Medicine, Alvin J. Siteman Cancer Center, St. Louis, Missouri
| | - Ryan C. Fields
- Division of General Surgery, Washington University School of Medicine, Alvin J. Siteman Cancer Center, St. Louis, Missouri
| | - Katherine A. Janeway
- Dana-Farber / Boston Children's Cancer and Blood Disorders Center, and Broad Institute of MIT and Harvard, Harvard Medical School, Boston, Massachusetts
| | - Bethany M. Kwan
- Department of Emergency Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Heinz-Josef Lenz
- Keck School of Medicine of USC, Norris Comprehensive Cancer Center, Los Angeles, California
| | - Qin Ma
- Department of Biomedical Informatics, The Ohio State University College of Medicine, Columbus, Ohio
| | - Shiraz I. Mishra
- Departments of Pediatrics and Family and Community Medicine, University of New Mexico Comprehensive Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, New Mexico
| | - Electra D. Paskett
- Division of Cancer Prevention and Control, Department of Internal Medicine, College of Medicine; Division of Epidemiology, College of Public Health, The Ohio State University, Columbus, Ohio
| | - Timothy R. Rebbeck
- Harvard TH Chan School of Public Health, Broad Institute of MIT and Harvard, and the Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Charité Ricker
- Division of Medical Oncology, Department of Medicine, Keck School of Medicine USC, Norris Comprehensive Cancer Center, Los Angeles, California
| | - Mariana C. Stern
- Department of Population and Public Health Sciences & Urology, Keck School of Medicine of USC, Norris Comprehensive Cancer Center, Los Angeles, California
| | - Andrew L. Sussman
- Department of Family and Community Medicine, University of New Mexico Comprehensive Cancer Center and Health Sciences Center, Albuquerque, New Mexico
| | - Jessica C. Tiner
- Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, Maryland
| | - Jeffrey M. Trent
- Translational Genomics Research Institute part of City of Hope, Phoenix, Arizona
| | - Roel GW. Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Nikhil Wagle
- Dana-Farber Cancer Institute, Broad Institute of MIT and Harvard, Harvard Medical School, Dana-Farber/Harvard Cancer Center, and Count Me In, Boston, Massachusetts
| | - Cheryl Willman
- Department of Laboratory Medicine and Pathology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, Minnesota
- University of New Mexico School of Medicine and Comprehensive Cancer Center, Albuquerque, New Mexico
| | - John FP. Bridges
- Department of Biomedical Informatics, The Ohio State University College of Medicine, Columbus, Ohio
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12
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Niada S, Varazzani A, Giannasi C, Fusco N, Armiraglio E, Di Bernardo A, Cherchi A, Baj A, Corradi D, Tafuni A, Parafioriti A, Ferrero S, Bianchi AE, Giannì AB, Poli T, Latif F, Brini AT. Significant association between FGFR1 mutation frequency and age in central giant cell granuloma. Pathology 2023; 55:329-334. [PMID: 36428107 DOI: 10.1016/j.pathol.2022.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/29/2022] [Accepted: 09/04/2022] [Indexed: 11/05/2022]
Abstract
Central giant cell granulomas (CGCG) are rare intraosseous osteolytic lesions of uncertain aetiology. Despite the benign nature of this neoplasia, the lesions can rapidly grow and become large, painful, invasive, and destructive. The identification of molecular drivers could help in the selection of targeted therapies for specific cases. TRPV4, KRAS and FGFR1 mutations have been associated with these lesions but no correlation between the mutations and patient features was observed so far. In this study, we analysed 17 CGCG cases of an Italian cohort and identified an interesting and significant (p=0.0021) correlation between FGFR1 mutations and age. In detail, FGFR1 mutations were observed frequently and exclusively in CGCG from young (<18 years old) patients (4/5 lesions, 80%). Furthermore, the combination between ours and previously published data confirmed a significant difference in the frequency of FGFR1 mutations in CGCG from patients younger than 18 years at the time of diagnosis (9/23 lesions, 39%) when compared to older patients (1/31 lesions, 0.03%; p=0.0011), thus corroborating our observation in a cohort of 54 patients. FGFR1 variants in young CGCG patients could favour fast lesion growth, implying that they seek medical attention earlier. Our observation might help prioritise candidates for FGFR1 testing, thus opening treatment options with FGFR inhibitors.
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Affiliation(s)
| | - Andrea Varazzani
- Maxillo-Facial Surgery, Head and Neck Department, University Hospital of Parma, Parma, Italy
| | - Chiara Giannasi
- IRCCS Istituto Ortopedico Galeazzi, Milan, Italy; Department of Biomedical, Surgical and Dental Sciences, Università degli Studi di Milano, Milan, Italy
| | - Nicola Fusco
- Division of Pathology, IEO, European Institute of Oncology IRCCS, Milan, Italy; Department of Oncology and Hematology-Oncology, University of Milan, Italy
| | | | - Andrea Di Bernardo
- Pathology Department, ASST Istituto Ortopedico Gaetano Pini - CTO, Milan, Italy
| | - Alessandro Cherchi
- Maxillo-Facial and Dental Unit, Fondazione Ca' Granda IRCCS Ospedale Maggiore Policlinico, Milan, Italy
| | - Alessandro Baj
- Department of Biomedical, Surgical and Dental Sciences, Università degli Studi di Milano, Milan, Italy; Maxillo-Facial and Dental Unit, Fondazione Ca' Granda IRCCS Ospedale Maggiore Policlinico, Milan, Italy
| | - Domenico Corradi
- Department of Medicine and Surgery, Unit of Pathology, University of Parma, Parma, Italy
| | - Alessandro Tafuni
- Department of Medicine and Surgery, Unit of Pathology, University of Parma, Parma, Italy
| | | | - Stefano Ferrero
- Department of Biomedical, Surgical and Dental Sciences, Università degli Studi di Milano, Milan, Italy; Division of Pathology, Fondazione IRCCS Cà Granda-Ospedale Maggiore Policlinico, Milan, Italy
| | - Andrea Edoardo Bianchi
- Istituto Stomatologico Italiano, Milan, Italy; Unicamillus, Saint Camillus Medical University, Rome, Italy
| | - Aldo Bruno Giannì
- Department of Biomedical, Surgical and Dental Sciences, Università degli Studi di Milano, Milan, Italy; Maxillo-Facial and Dental Unit, Fondazione Ca' Granda IRCCS Ospedale Maggiore Policlinico, Milan, Italy
| | - Tito Poli
- Maxillo-Facial Surgery, Head and Neck Department, University Hospital of Parma, Parma, Italy
| | - Farida Latif
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences University of Birmingham, Edgbaston, Birmingham, UK
| | - Anna Teresa Brini
- IRCCS Istituto Ortopedico Galeazzi, Milan, Italy; Department of Biomedical, Surgical and Dental Sciences, Università degli Studi di Milano, Milan, Italy
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13
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Marx O, Mankarious M, Yochum G. Molecular genetics of early-onset colorectal cancer. World J Biol Chem 2023; 14:13-27. [PMID: 37034132 PMCID: PMC10080548 DOI: 10.4331/wjbc.v14.i2.13] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/20/2022] [Accepted: 02/13/2023] [Indexed: 03/24/2023] Open
Abstract
Early-onset colorectal cancer (EOCRC) has been rising in global prevalence and incidence over the past several decades. Environmental influences, including generational lifestyle changes and rising obesity, contribute to these increased rates. While the rise in EOCRC is best documented in western countries, it is seen throughout the world, although EOCRC may have distinct genetic mutations in patients of different ethnic backgrounds. Pathological and molecular characterizations show that EOCRC has a distinct presentation compared with later-onset colorectal cancer (LOCRC). Recent studies have identified DNA, RNA, and protein-level alterations unique to EOCRC, revealing much-needed biomarkers and potential novel therapeutic targets. Many molecular EOCRC studies have been performed with Caucasian and Asian EOCRC cohorts, however, studies of other ethnic backgrounds are limited. In addition, certain molecular characterizations that have been conducted for LOCRC have not yet been repeated in EOCRC, including high-throughput analyses of histone modifications, mRNA splicing, and proteomics on large cohorts. We propose that the complex relationship between cancer and aging should be considered when studying the molecular underpinnings of EOCRC. In this review, we summarize current EOCRC literature, focusing on sporadic molecular alterations in tumors, and their clinical implications. We conclude by discussing current challenges and future directions of EOCRC research efforts.
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Affiliation(s)
- Olivia Marx
- Department of Biochemistry & Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA 17033, United States
| | - Marc Mankarious
- Department of Surgery, Division of Colon & Rectal Surgery, Pennsylvania State University Milton S. Hershey Medical Center, Hershey, PA 17033, United States
| | - Gregory Yochum
- Department of Biochemistry & Molecular Biology & Surgery, Pennsylvania State University College of Medicine, Hershey, PA 17033, United States
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14
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Schuster ALR, Hampel H, Paskett ED, Bridges JFP. Rethinking Patient Engagement in Cancer Research. THE PATIENT 2023; 16:89-93. [PMID: 36301439 PMCID: PMC9911482 DOI: 10.1007/s40271-022-00604-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Accepted: 09/20/2022] [Indexed: 01/19/2023]
Affiliation(s)
- Anne L R Schuster
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Lincoln Tower, 1800 Cannon Drive, Columbus, OH, USA.
| | - Heather Hampel
- Division of Clinical Cancer Genomics, City of Hope National Medical Center, Duarte, CA, USA.,Division of Human Genetics, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Electra D Paskett
- Division of Cancer Prevention and Control, Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH, USA.,Division of Epidemiology, College of Public Health, The Ohio State University, Columbus, OH, USA
| | - John F P Bridges
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Lincoln Tower, 1800 Cannon Drive, Columbus, OH, USA
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15
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Chan A, Cheng I, Wang C, Tan CJ, Toh YL, Ng DQ, Koh YQ, Zhou H, Foo KM, Chan RJ, Ho HK, Chew L, Farid M, Tannock I. Cognitive impairment in adolescent and young adult cancer patients: Pre-treatment findings of a longitudinal study. Cancer Med 2023; 12:4821-4831. [PMID: 36221816 PMCID: PMC9972136 DOI: 10.1002/cam4.5295] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 09/08/2022] [Accepted: 09/16/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND There is little information about cancer-related cognitive impairment (CRCI) in adolescent and young adults (AYA, 15-39 years old) due to its rare incidence. Here, we present the pre-treatment (before chemotherapy or radiotherapy) evaluation of cognitive function and ability of AYA with cancer (AYAC) in a multicentered cohort study. METHODS Newly diagnosed AYAC and age-matched healthy controls (HC) were recruited between 2018 and 2021. The primary outcome was the comparison of pre-treatment cognitive impairment defined as 2 standard deviations (SDs) below the HC on ≥1 cognitive test, or >1.5 SDs below on ≥2 tests using CANTAB® between AYAC and HC. Secondary outcomes included self-perceived cognitive ability assessed by FACT-Cog v3 and biomarkers (inflammatory cytokines and brain-derived neurotrophic factor [BDNF]). RESULTS We recruited 74 AYAC (median age = 34) and 118 HC (median age = 32). On objective cognitive testing, we observed three times more AYAC patients performed poorly on at least 2 cognitive tests compared to HC (40.5% vs. 13.6%, p < 0.001). AYAC self-perceived less degree of cognitive impairment than HC (p < 0.001). However, AYAC perceived a greater impact of cognitive changes on their quality of life compared to HC (p = 0.039). Elevated baseline inflammatory markers (IL-2, IL-4, IL-6, IL-8, IL-10 and IFN-γ) were observed among AYAC compared to HC, and baseline BDNF was lower in AYAC compared to HC. Interaction effects between cancer diagnosis and biomarkers were observed in predicting cognitive function. CONCLUSION With the pre-existence of CRCI and risk factors of neuroinflammation even prior to systemic therapy, AYAC should receive early rehabilitation to prevent further deterioration of cognitive function after initiation of systemic therapies. (ClinicalTrials.gov Identifier: NCT03476070).
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Affiliation(s)
- Alexandre Chan
- Department of Clinical Pharmacy Practice, University of California Irvine, Irvine, California, USA.,Department of Pharmacy, National Cancer Centre Singapore, Singapore
| | - Ivy Cheng
- Department of Pharmacy, National Cancer Centre Singapore, Singapore
| | - Claire Wang
- Department of Pharmacy, National University of Singapore, Singapore
| | - Chia Jie Tan
- Department of Pharmacy, National University of Singapore, Singapore
| | - Yi Long Toh
- Department of Pharmacy, National University of Singapore, Singapore
| | - Ding Quan Ng
- Department of Clinical Pharmacy Practice, University of California Irvine, Irvine, California, USA
| | - Yong Qin Koh
- Department of Pharmacy, National University of Singapore, Singapore
| | - Hanzhang Zhou
- Department of Pharmacy, National University of Singapore, Singapore
| | - Koon Mian Foo
- Department of Pharmacy, KK Women and Children's Hospital, Singapore
| | - Raymond Javan Chan
- Caring Futures Institutes, College of Nursing and Health Sciences, Flinders University, Adelaide, South Australia, Australia
| | - Han Kiat Ho
- Department of Pharmacy, National University of Singapore, Singapore
| | - Lita Chew
- Department of Pharmacy, National Cancer Centre Singapore, Singapore.,Department of Pharmacy, National University of Singapore, Singapore
| | - Mohamad Farid
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Ian Tannock
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
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16
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Wang X, Langevin AM, Houghton PJ, Zheng S. Genomic disparities between cancers in adolescent and young adults and in older adults. Nat Commun 2022; 13:7223. [PMID: 36433963 PMCID: PMC9700745 DOI: 10.1038/s41467-022-34959-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 11/11/2022] [Indexed: 11/27/2022] Open
Abstract
Cancers cause significant mortality and morbidity in adolescents and young adults (AYAs), but their biological underpinnings are incompletely understood. Here, we analyze clinical and genomic disparities between AYAs and older adults (OAs) in more than 100,000 cancer patients. We find significant differences in clinical presentation between AYAs and OAs, including sex, metastasis rates, race and ethnicity, and cancer histology. In most cancer types, AYA tumors show lower mutation burden and less genome instability. Accordingly, most cancer genes show less mutations and copy number changes in AYAs, including the noncoding TERT promoter mutations. However, CTNNB1 and BRAF mutations are consistently overrepresented in AYAs across multiple cancer types. AYA tumors also exhibit more driver gene fusions that are frequently observed in pediatric cancers. We find that histology is an important contributor to genetic disparities between AYAs and OAs. Mutational signature analysis of hypermutators shows stronger endogenous mutational processes such as MMR-deficiency but weaker exogenous processes such as tobacco exposure in AYAs. Finally, we demonstrate a panoramic view of clinically actionable genetic events in AYA tumors.
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Affiliation(s)
- Xiaojing Wang
- grid.267309.90000 0001 0629 5880Greehey Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX USA ,grid.267309.90000 0001 0629 5880Department of Population Health Sciences, UT Health San Antonio, San Antonio, TX USA ,grid.267309.90000 0001 0629 5880MD Anderson Mays Cancer Center, UT Health San Antonio, San Antonio, TX USA
| | - Anne-Marie Langevin
- grid.267309.90000 0001 0629 5880MD Anderson Mays Cancer Center, UT Health San Antonio, San Antonio, TX USA ,grid.267309.90000 0001 0629 5880Department of Pediatrics, UT Health San Antonio, San Antonio, TX USA
| | - Peter J. Houghton
- grid.267309.90000 0001 0629 5880Greehey Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX USA ,grid.267309.90000 0001 0629 5880MD Anderson Mays Cancer Center, UT Health San Antonio, San Antonio, TX USA ,grid.267309.90000 0001 0629 5880Department of Molecular Medicine, UT Health San Antonio, San Antonio, TX USA
| | - Siyuan Zheng
- grid.267309.90000 0001 0629 5880Greehey Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX USA ,grid.267309.90000 0001 0629 5880Department of Population Health Sciences, UT Health San Antonio, San Antonio, TX USA ,grid.267309.90000 0001 0629 5880MD Anderson Mays Cancer Center, UT Health San Antonio, San Antonio, TX USA
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17
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Chatsirisupachai K, Lagger C, de Magalhães JP. Age-associated differences in the cancer molecular landscape. Trends Cancer 2022; 8:962-971. [PMID: 35811230 DOI: 10.1016/j.trecan.2022.06.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/11/2022] [Accepted: 06/13/2022] [Indexed: 12/24/2022]
Abstract
Cancer is an age-related disease, as incidence and mortality for most types of cancer increase with age. However, how molecular alterations in tumors differ among patients of different ages remains poorly understood. Recent studies have shed light on the age-associated molecular landscapes in cancer. Here, we summarize the main findings of these current studies, highlighting major differences in the genomic, transcriptomic, epigenetic, and immunological landscapes between cancer in younger and older patients. Importantly, some cancer driver genes are mutated more frequently in younger or older patients. We discuss the potential roles of aging-related processes in shaping these age-related differences in cancer. We further emphasize the remaining unsolved questions that could provide important insights that will have implications in personalized medicine.
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Affiliation(s)
- Kasit Chatsirisupachai
- Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK.
| | - Cyril Lagger
- Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK
| | - João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK.
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18
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How Genetics and Genomics Advances Are Rewriting Pediatric Cancer Research and Clinical Care. Medicina (B Aires) 2022; 58:medicina58101386. [PMID: 36295546 PMCID: PMC9610804 DOI: 10.3390/medicina58101386] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/28/2022] [Accepted: 09/28/2022] [Indexed: 11/17/2022] Open
Abstract
In the last two decades, thanks to the data that have been obtained from the Human Genome Project and the development of next-generation sequencing (NGS) technologies, research in oncology has produced extremely important results in understanding the genomic landscape of pediatric cancers, which are the main cause of death during childhood. NGS has provided significant advances in medicine by detecting germline and somatic driver variants that determine the development and progression of many types of cancers, allowing a distinction between hereditary and non-hereditary cancers, characterizing resistance mechanisms that are also related to alterations of the epigenetic apparatus, and quantifying the mutational burden of tumor cells. A combined approach of next-generation technologies allows us to investigate the numerous molecular features of the cancer cell and the effects of the environment on it, discovering and following the path of personalized therapy to defeat an "ancient" disease that has had victories and defeats. In this paper, we provide an overview of the results that have been obtained in the last decade from genomic studies that were carried out on pediatric cancer and their contribution to the more accurate and faster diagnosis in the stratification of patients and the development of new precision therapies.
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19
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Marx OM, Mankarious MM, Eshelman MA, Ding W, Koltun WA, Yochum GS. Transcriptome Analyses Identify Deregulated MYC in Early Onset Colorectal Cancer. Biomolecules 2022; 12:1223. [PMID: 36139061 PMCID: PMC9496520 DOI: 10.3390/biom12091223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/23/2022] [Accepted: 08/30/2022] [Indexed: 11/21/2022] Open
Abstract
Despite a global decrease in colorectal cancer (CRC) incidence, the prevalence of early-onset colorectal cancer (EOCRC), or those occurring in individuals before the age of 50, has steadily increased over the past several decades. When compared to later onset colorectal cancer (LOCRC) in individuals over 50, our understanding of the genetic and molecular underpinnings of EOCRCs is limited. Here, we conducted transcriptomic analyses of patient-matched normal colonic segments and tumors to identify gene expression programs involved in carcinogenesis. Amongst differentially expressed genes, we found increased expression of the c-MYC proto-oncogene (MYC) and its downstream targets in tumor samples. We identified tumors with high and low differential MYC expression and found patients with high-MYC tumors were older and overweight or obese. We also detected elevated expression of the PVT1 long-non-coding RNA (lncRNA) in most tumors and found gains in copy number for both MYC and PVT1 gene loci in 35% of tumors evaluated. Our transcriptome analyses indicate that EOCRC can be sub-classified into groups based on differential MYC expression and suggest that deregulated MYC contributes to CRCs that develop in younger patients.
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Affiliation(s)
- Olivia M. Marx
- Department of Biochemistry & Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
- Department of Surgery, Division of Colon & Rectal Surgery, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Marc M. Mankarious
- Department of Surgery, Division of Colon & Rectal Surgery, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Melanie A. Eshelman
- Department of Pediatrics, Division of Hematology & Oncology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Wei Ding
- Department of Surgery, Division of Colon & Rectal Surgery, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Walter A. Koltun
- Department of Surgery, Division of Colon & Rectal Surgery, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Gregory S. Yochum
- Department of Biochemistry & Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
- Department of Surgery, Division of Colon & Rectal Surgery, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
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20
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Lumish MA, Cercek A. Practical Considerations in Diagnosing and Managing Early-Onset GI Cancers. J Clin Oncol 2022; 40:2662-2680. [PMID: 35839438 PMCID: PMC9390825 DOI: 10.1200/jco.21.02708] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 03/12/2022] [Accepted: 04/18/2022] [Indexed: 12/24/2022] Open
Abstract
The incidence of early-onset (EO) GI cancers occurring in individuals younger than age 50 years has been rising at an alarming rate over the past two decades. Although this rise in incidence among young patients correlates with increased rates of obesity, changes in diet, and alterations in the environment, the effects of these environmental factors on carcinogenesis, metastasis, and treatment response are unknown. Although several unique clinical trends exist among EO-GI cancers and their average-onset GI cancer counterparts, GI cancers are molecularly indistinct between younger and older patients, and no data support distinct treatment paradigms for patients with EO disease. The majority of EO-GI cancers are not explained by germline changes. There remains a critical need for further research to understand the pathogenesis and optimal management of EO-GI cancers. In addition, current screening strategies are not adequate to identify EO-GI cancers, and early biomarkers are needed. Specialized centers, with a focus on psychosocial aspects of cancer management, can address the unique care needs of patients with EO-GI cancers.
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Affiliation(s)
- Melissa A. Lumish
- Memorial Sloan Kettering Cancer Center, Department of Medicine, New York, NY
| | - Andrea Cercek
- Memorial Sloan Kettering Cancer Center, Department of Medicine, New York, NY
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21
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Kumar R, Abreu C, Toi M, Saini S, Casimiro S, Arora A, Paul AM, Velaga R, Rameshwar P, Lipton A, Gupta S, Costa L. Oncobiology and treatment of breast cancer in young women. Cancer Metastasis Rev 2022; 41:749-770. [PMID: 35488982 DOI: 10.1007/s10555-022-10034-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 04/14/2022] [Indexed: 12/20/2022]
Abstract
Female breast cancer emerged as the leading cancer type in terms of incidence globally in 2020. Although mortality due to breast cancer has improved during the past three decades in many countries, this trend has reversed in women less than 40 years since the past decade. From the biological standpoint, there is consensus among experts regarding the clinically relevant definition of breast cancer in young women (BCYW), with an age cut-off of 40 years. The idea that breast cancer is an aging disease has apparently broken in the case of BCYW due to the young onset and an overall poor outcome of BCYW patients. In general, younger patients exhibit a worse prognosis than older pre- and postmenopausal patients due to the aggressive nature of cancer subtypes, a high percentage of cases with advanced stages at diagnosis, and a high risk of relapse and death in younger patients. Because of clinically and biologically unique features of BCYW, it is suspected to represent a distinct biologic entity. It is unclear why BCYW is more aggressive and has an inferior prognosis with factors that contribute to increased incidence. However, unique developmental features, adiposity and immune components of the mammary gland, hormonal interplay and crosstalk with growth factors, and a host of intrinsic and extrinsic risk factors and cellular regulatory interactions are considered to be the major contributing factors. In the present article, we discuss the status of BCYW oncobiology, therapeutic interventions and considerations, current limitations in fully understanding the basis and underlying cause(s) of BCYW, understudied areas of BCYW research, and postulated advances in the coming years for the field.
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Affiliation(s)
- Rakesh Kumar
- Cancer Research Institute, Himalayan Institute of Medical Sciences, Swami Rama Himalayan University, Dehradun, India. .,Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India. .,Department of Medicine, Division of Hematology and Oncology, Rutgers New Jersey Medical School, Newark, NJ, USA. .,Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, VA, USA.
| | - Catarina Abreu
- Department of Medical Oncology, Hospital de Santa Maria- Centro Hospitalar Universitário Lisboa Norte, Lisbon, Portugal
| | - Masakazu Toi
- Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Sunil Saini
- Cancer Research Institute, Himalayan Institute of Medical Sciences, Swami Rama Himalayan University, Dehradun, India
| | - Sandra Casimiro
- Instituto de Medicina Molecular-João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
| | - Anshika Arora
- Cancer Research Institute, Himalayan Institute of Medical Sciences, Swami Rama Himalayan University, Dehradun, India
| | - Aswathy Mary Paul
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
| | - Ravi Velaga
- Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Pranela Rameshwar
- Department of Medicine, Division of Hematology and Oncology, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Allan Lipton
- Hematology-Oncology, Department of Medicine, Penn State University School of Medicine, Hershey, PA, USA
| | - Sudeep Gupta
- Department of Medical Oncology, Tata Memorial Centre and Homi Bhabha National Institute, Mumbai, India
| | - Luis Costa
- Department of Medical Oncology, Hospital de Santa Maria- Centro Hospitalar Universitário Lisboa Norte, Lisbon, Portugal.,Instituto de Medicina Molecular-João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
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22
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Yehia L, Eng C. One Size Does Not Fit All: Breast Cancer in Young Women. Clin Cancer Res 2022; 28:2209-2210. [PMID: 35320364 DOI: 10.1158/1078-0432.ccr-22-0352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/06/2022] [Accepted: 03/14/2022] [Indexed: 11/16/2022]
Abstract
Breast cancers occurring in young women remain poorly characterized. Through studying a series of very young women with breast cancer compared to older women with breast cancer, distinct biological features were identified, with important implications for the personalized genomics-driven management of these cancers.
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Affiliation(s)
- Lamis Yehia
- Cleveland Clinic, Cleveland, OH, United States
| | - Charis Eng
- Cleveland Clinic, Cleveland, OH, United States
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