1
|
Shao J, Xu Y, Olsen RJ, Kasparian S, Sun K, Mathur S, Zhang J, He C, Chen SH, Bernicker EH, Li Z. 5-Hydroxymethylcytosine in Cell-Free DNA Predicts Immunotherapy Response in Lung Cancer. Cells 2024; 13:715. [PMID: 38667328 PMCID: PMC11049556 DOI: 10.3390/cells13080715] [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: 02/21/2024] [Revised: 04/04/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
Immune checkpoint inhibitors (ICIs) drastically improve therapeutic outcomes for lung cancer, but accurately predicting individual patient responses to ICIs remains a challenge. We performed the genome-wide profiling of 5-hydroxymethylcytosine (5hmC) in 85 plasma cell-free DNA (cfDNA) samples from lung cancer patients and developed a 5hmC signature that was significantly associated with progression-free survival (PFS). We built a 5hmC predictive model to quantify the 5hmC level and validated the model in the validation, test, and control sets. Low weighted predictive scores (wp-scores) were significantly associated with a longer PFS compared to high wp-scores in the validation [median 7.6 versus 1.8 months; p = 0.0012; hazard ratio (HR) 0.12; 95% confidence interval (CI), 0.03-0.54] and test (median 14.9 versus 3.3 months; p = 0.00074; HR 0.10; 95% CI, 0.02-0.50) sets. Objective response rates in patients with a low or high wp-score were 75.0% (95% CI, 42.8-94.5%) versus 0.0% (95% CI, 0.0-60.2%) in the validation set (p = 0.019) and 80.0% (95% CI, 44.4-97.5%) versus 0.0% (95% CI, 0.0-36.9%) in the test set (p = 0.0011). The wp-scores were also significantly associated with PFS in patients receiving single-agent ICI treatment (p < 0.05). In addition, the 5hmC predictive signature demonstrated superior predictive capability to tumor programmed death-ligand 1 and specificity to ICI treatment response prediction. Moreover, we identified novel 5hmC-associated genes and signaling pathways integral to ICI treatment response in lung cancer. This study provides proof-of-concept evidence that the cfDNA 5hmC signature is a robust biomarker for predicting ICI treatment response in lung cancer.
Collapse
Affiliation(s)
- Jianming Shao
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA (R.J.O.)
- Houston Methodist Research Institute, Houston, TX 77030, USA (S.M.); (S.-H.C.)
| | - Yitian Xu
- Houston Methodist Research Institute, Houston, TX 77030, USA (S.M.); (S.-H.C.)
| | - Randall J. Olsen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA (R.J.O.)
- Houston Methodist Research Institute, Houston, TX 77030, USA (S.M.); (S.-H.C.)
- Weill Cornell Medical College, New York, NY 10065, USA
| | - Saro Kasparian
- Neal Cancer Center, Houston Methodist Hospital, Houston, TX 77030, USA (E.H.B.)
- Department of Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Kai Sun
- Weill Cornell Medical College, New York, NY 10065, USA
- Neal Cancer Center, Houston Methodist Hospital, Houston, TX 77030, USA (E.H.B.)
| | - Sunil Mathur
- Houston Methodist Research Institute, Houston, TX 77030, USA (S.M.); (S.-H.C.)
- Neal Cancer Center, Houston Methodist Hospital, Houston, TX 77030, USA (E.H.B.)
| | - Jun Zhang
- Weill Cornell Medical College, New York, NY 10065, USA
- Neal Cancer Center, Houston Methodist Hospital, Houston, TX 77030, USA (E.H.B.)
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Shu-Hsia Chen
- Houston Methodist Research Institute, Houston, TX 77030, USA (S.M.); (S.-H.C.)
- Neal Cancer Center, Houston Methodist Hospital, Houston, TX 77030, USA (E.H.B.)
| | - Eric H. Bernicker
- Neal Cancer Center, Houston Methodist Hospital, Houston, TX 77030, USA (E.H.B.)
| | - Zejuan Li
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA (R.J.O.)
- Houston Methodist Research Institute, Houston, TX 77030, USA (S.M.); (S.-H.C.)
- Weill Cornell Medical College, New York, NY 10065, USA
| |
Collapse
|
2
|
Vayani OR, Kaufman ME, Moore K, Chennakesavalu M, TerHaar R, Chaves G, Chlenski A, He C, Cohn SL, Applebaum MA. Adrenergic and mesenchymal signatures are identifiable in cell-free DNA and correlate with metastatic disease burden in children with neuroblastoma. Pediatr Blood Cancer 2024; 71:e30735. [PMID: 37859597 PMCID: PMC10842006 DOI: 10.1002/pbc.30735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/07/2023] [Accepted: 10/09/2023] [Indexed: 10/21/2023]
Abstract
BACKGROUND Cell-free DNA (cfDNA) profiles of 5-hydroxymethylcytosine (5-hmC), an epigenetic marker of open chromatin and active gene expression, are correlated with metastatic disease burden in patients with neuroblastoma. Neuroblastoma tumors are comprised of adrenergic (ADRN) and mesenchymal (MES) cells, and the relative abundance of each in tumor biopsies has prognostic implications. We hypothesized that ADRN and MES-specific signatures could be quantified in cfDNA 5-hmC profiles and would augment the detection of metastatic burden in patients with neuroblastoma. METHODS We previously performed an integrative analysis to identify ADRN and MES-specific genes (n = 373 and n = 159, respectively). Purified DNA from cell lines was serial diluted with healthy donor cfDNA. Using Gene Set Variation Analysis (GSVA), ADRN and MES signatures were optimized. We then quantified signature scores, and our prior neuroblastoma signature, in cfDNA from 84 samples from 46 high-risk patients including 21 patients with serial samples. RESULTS Samples from patients with higher metastatic burden had increased GSVA scores for both ADRN and MES gene signatures (p < .001). While ADRN and MES signature scores tracked together in serially collected samples, we identified instances of patients with increases in either MES or ADRN score at relapse. CONCLUSIONS While it is feasible to identify ADRN and MES signatures using 5-hmC profiles of cfDNA from neuroblastoma patients and correlate these signatures to metastatic burden, additional data are needed to determine the optimal strategies for clinical implementation. Prospective evaluation in larger cohorts is ongoing.
Collapse
Affiliation(s)
- Omar R Vayani
- Pritzker School of Medicine, The University of Chicago, Chicago, Illinois, USA
| | - Maria E Kaufman
- Pritzker School of Medicine, The University of Chicago, Chicago, Illinois, USA
| | - Kelley Moore
- Department of Pediatrics, Section of Hematology/Oncology, The University of Chicago, Chicago, Illinois, USA
| | | | - Rachel TerHaar
- Department of Pediatrics, Section of Hematology/Oncology, The University of Chicago, Chicago, Illinois, USA
| | - Gepoliano Chaves
- Department of Pediatrics, Section of Hematology/Oncology, The University of Chicago, Chicago, Illinois, USA
| | - Alexandre Chlenski
- Department of Pediatrics, Section of Hematology/Oncology, The University of Chicago, Chicago, Illinois, USA
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, Illinois, USA
| | - Susan L Cohn
- Department of Pediatrics, Section of Hematology/Oncology, The University of Chicago, Chicago, Illinois, USA
| | - Mark A Applebaum
- Department of Pediatrics, Section of Hematology/Oncology, The University of Chicago, Chicago, Illinois, USA
| |
Collapse
|
3
|
Vayani OR, Kaufman ME, Moore K, Chennakesavalu M, TerHaar R, Chaves G, Chlenski A, He C, Cohn SL, Applebaum MA. Adrenergic and mesenchymal signatures are identifiable in cell-free DNA and correlate with metastatic disease burden in children with neuroblastoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.30.554943. [PMID: 37693610 PMCID: PMC10491182 DOI: 10.1101/2023.08.30.554943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Background Cell free DNA (cfDNA) profiles of 5-hydroxymethylcytosine (5-hmC), an epigenetic marker of open chromatin and active gene expression, are correlated with metastatic disease burden in patients with neuroblastoma. Neuroblastoma tumors are comprised of adrenergic (ADRN) and mesenchymal (MES) cells, and the relative abundance of each in tumor biopsies has prognostic implications. We hypothesized that ADRN and MES specific signatures could be quantified in cfDNA 5-hmC profiles and would augment the detection of metastatic burden in patients with neuroblastoma. Methods We previously performed an integrative analysis to identify ADRN and MES specific genes (n=373 and n=159, respectively). Purified DNA from cell lines was serial diluted with healthy donor cfDNA. Using Gene Set Variation Analysis (GSVA), ADRN and MES signatures were optimized. We then quantified signature scores, and our prior neuroblastoma signature, in cfDNA from 84 samples from 46 high-risk patients including 21 patients with serial samples. Results Samples from patients with higher metastatic burden had increased GSVA scores for both ADRN and MES gene signatures (p < 0.001). While ADRN and MES signature scores tracked together in serially collected samples, we identified instances of patients with increases in either MES or ADRN score at relapse. Conclusions While it is feasible to identify ADRN and MES signatures using 5-hmC profiles of cfDNA from neuroblastoma patients and correlate these signatures to metastatic burden, additional data are needed to determine the optimal strategies for clinical implementation. Prospective evaluation in larger cohorts is ongoing.
Collapse
|
4
|
Chennakesavalu M, Moore K, Chaves G, Veeravalli S, TerHaar R, Wu T, Lyu R, Chlenski A, He C, Piunti A, Applebaum MA. 5-hydroxymethylcytosine profiling of cell-free DNA identifies bivalent genes that are prognostic of survival in high-risk neuroblastoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.27.538309. [PMID: 37163024 PMCID: PMC10168384 DOI: 10.1101/2023.04.27.538309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Neuroblastoma is the most common extra-cranial solid tumor in childhood and epigenetic dysregulation is a key driver of this embryonal disease. In cell-free DNA from neuroblastoma patients with high-risk disease, we found increased 5-hydroxymethylcytosine (5-hmC) deposition on Polycomb Repressive Complex 2 (PRC2) target genes, a finding previously described in the context of bivalent genes. As bivalent genes, defined as genes bearing both activating (H3K4me3) and repressive (H3K27me3) chromatin modifications, have been shown to play an important role in development and cancer, we investigated the potential role of bivalent genes in maintaining a de-differentiated state in neuroblastoma and their potential use as a biomarker. We identified 313 genes that bore bivalent chromatin marks, were enriched for mediators of neuronal differentiation, and were transcriptionally repressed across a panel of heterogenous neuroblastoma cell lines. Through gene set variance analysis, we developed a clinically implementable bivalent signature. In three distinct clinical cohorts, low bivalent signature was significantly and independently associated with worse clinical outcome in high-risk neuroblastoma patients. Thus, low expression of bivalent genes is a biomarker of ultra-high-risk disease and may represent a therapeutic opportunity in neuroblastoma.
Collapse
|
5
|
Zhou M, Hou P, Yan C, Chen L, Li K, Wang Y, Zhao J, Su J, Sun J. Cell-free DNA 5-hydroxymethylcytosine profiles of long non-coding RNA genes enable early detection and progression monitoring of human cancers. Clin Epigenetics 2021; 13:197. [PMID: 34689838 PMCID: PMC8543867 DOI: 10.1186/s13148-021-01183-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/11/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND 5-Hydroxymethylcytosine (5hmC) is a significant DNA epigenetic modification. However, the 5hmC modification alterations in genomic regions encoding long non-coding RNA (lncRNA) and their clinical significance remain poorly characterized. RESULTS A three-phase discovery-modeling-validation study was conducted to explore the potential of the plasma-derived 5hmC modification level in genomic regions encoding lncRNAs as a superior alternative biomarker for cancer diagnosis and surveillance. Genome-wide 5hmC profiles in the plasma circulating cell-free DNA of 1632 cancer and 1379 non-cancerous control samples from different cancer types and multiple centers were repurposed and characterized. A large number of altered 5hmC modifications were distributed at genomic regions encoding lncRNAs in cancerous compared with healthy subjects. Furthermore, most 5hmC-modified lncRNA genes were cancer-specific, with only a relatively small number of 5hmC-modified lncRNA genes shared by various cancer types. A 5hmC-LncRNA diagnostic score (5hLD-score) comprising 39 tissue-shared 5hmC-modified lncRNA gene markers was developed using elastic net regularization. The 5hLD-score was able to accurately distinguish tumors from healthy controls with an area under the curve (AUC) of 0.963 [95% confidence interval (CI) 0.940-0.985] and 0.912 (95% CI 0.837-0.987) in the training and internal validation cohorts, respectively. Results from three independent validations confirmed the robustness and stability of the 5hLD-score with an AUC of 0.851 (95% CI 0.786-0.916) in Zhang's non-small cell lung cancer cohort, AUC of 0.887 (95% CI 0.852-0.922) in Tian's esophageal cancer cohort, and AUC of 0.768 (95% CI 0.746-0.790) in Cai's hepatocellular carcinoma cohort. In addition, a significant association was identified between the 5hLD-score and the progression from hepatitis to liver cancer. Finally, lncRNA genes modified by tissue-specific 5hmC alteration were again found to be capable of identifying the origin and location of tumors. CONCLUSION The present study will contribute to the ongoing effort to understand the transcriptional programs of lncRNA genes, as well as facilitate the development of novel invasive genomic tools for early cancer detection and surveillance.
Collapse
Affiliation(s)
- Meng Zhou
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Ping Hou
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Congcong Yan
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Lu Chen
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Ke Li
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Yiran Wang
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Jingting Zhao
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Jianzhong Su
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China.
| | - Jie Sun
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China.
| |
Collapse
|
6
|
Narmontė M, Gibas P, Daniūnaitė K, Gordevičius J, Kriukienė E. Multiomics Analysis of Neuroblastoma Cells Reveals a Diversity of Malignant Transformations. Front Cell Dev Biol 2021; 9:727353. [PMID: 34557494 PMCID: PMC8452964 DOI: 10.3389/fcell.2021.727353] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/12/2021] [Indexed: 12/12/2022] Open
Abstract
Neuroblastoma (NB) is a pediatric cancer of the developing sympathetic nervous system that exhibits significant variation in the stage of differentiation and cell composition of tumors. Global loss of DNA methylation and genomic 5-hydroxymethylcytosine (5hmC) is a hallmark of human cancers. Here, we used our recently developed single-base resolution approaches, hmTOP-seq and uTOP-seq, for construction of 5hmC maps and identification of large partially methylated domains (PMDs) in different NB cell subpopulations. The 5hmC profiles revealed distinct signatures characteristic to different cell lineages and stages of malignant transformation of NB cells in a conventional and oxygen-depleted environment, which often occurs in tumors. The analysis of the cell-type-specific PMD distribution highlighted differences in global genome organization among NB cells that were ascribed to the same lineage identity by transcriptomic networks. Collectively, we demonstrated a high informativeness of the integrative epigenomic and transcriptomic research and large-scale genome structure in investigating the mechanisms that regulate cell identities and developmental stages of NB cells. Such multiomics analysis, as compared with mutational studies, open new ways for identification of novel disease-associated features which bring prognostic and therapeutic value in treating this aggressive pediatric disease.
Collapse
Affiliation(s)
- Milda Narmontė
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Povilas Gibas
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Kristina Daniūnaitė
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.,Human Genome Research Group, Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Juozas Gordevičius
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Edita Kriukienė
- Department of Biological DNA Modification, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| |
Collapse
|
7
|
Chen HY, Zhang WL, Zhang L, Yang P, Li F, Yang ZR, Wang J, Pang M, Hong Y, Yan C, Li W, Liu J, Xu N, Chen L, Xiao XB, Qin Y, He XH, Liu H, Zhu HC, He C, Lin J, Jing HM. 5-Hydroxymethylcytosine profiles of cfDNA are highly predictive of R-CHOP treatment response in diffuse large B cell lymphoma patients. Clin Epigenetics 2021; 13:33. [PMID: 33573703 PMCID: PMC7879534 DOI: 10.1186/s13148-020-00973-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 11/09/2020] [Indexed: 02/06/2023] Open
Abstract
Background Although R-CHOP (rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone) remains the standard chemotherapy regimen for diffuse large B cell lymphoma (DLBCL) patients, not all patients are responsive to the scheme, and there is no effective method to predict treatment response. Methods We utilized 5hmC-Seal to generate genome-wide 5hmC profiles in plasma cell-free DNA (cfDNA) from 86 DLBCL patients before they received R-CHOP chemotherapy. To investigate the correlation between 5hmC modifications and curative effectiveness, we separated patients into training (n = 56) and validation (n = 30) cohorts and developed a 5hmC-based logistic regression model from the training cohort to predict the treatment response in the validation cohort. Results In this study, we identified thirteen 5hmC markers associated with treatment response. The prediction performance of the logistic regression model, achieving 0.82 sensitivity and 0.75 specificity (AUC = 0.78), was superior to existing clinical indicators, such as LDH and stage. Conclusions Our findings suggest that the 5hmC modifications in cfDNA at the time before R-CHOP treatment are associated with treatment response and that 5hmC-Seal may potentially serve as a clinical-applicable, minimally invasive approach to predict R-CHOP treatment response for DLBCL patients.
Collapse
Affiliation(s)
- Hang-Yu Chen
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Innovation Center for Genomics, Peking University, Beijing, 100871, People's Republic of China
| | - Wei-Long Zhang
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, Beijing, 100191, People's Republic of China
| | - Lei Zhang
- Yang Sheng Tang Natural Medicine Research Institute, Hangzhou, 310024, People's Republic of China
| | - Ping Yang
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, Beijing, 100191, People's Republic of China
| | - Fang Li
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, Beijing, 100191, People's Republic of China
| | - Ze-Ruo Yang
- Yang Sheng Tang Natural Medicine Research Institute, Hangzhou, 310024, People's Republic of China
| | - Jing Wang
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, Beijing, 100191, People's Republic of China
| | - Meng Pang
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, Beijing, 100191, People's Republic of China
| | - Yun Hong
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, Beijing, 100191, People's Republic of China
| | - Changjian Yan
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, Beijing, 100191, People's Republic of China
| | - Wei Li
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, Beijing, 100191, People's Republic of China
| | - Jia Liu
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, Beijing, 100191, People's Republic of China
| | - Nuo Xu
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Innovation Center for Genomics, Peking University, Beijing, 100871, People's Republic of China
| | - Long Chen
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Innovation Center for Genomics, Peking University, Beijing, 100871, People's Republic of China
| | - Xiu-Bing Xiao
- Lymphoma Head and Neck Oncology, Fifth Medical Center of PLA General Hospital, Beijing, 100039, People's Republic of China
| | - Yan Qin
- Department of Medical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, People's Republic of China
| | - Xiao-Hui He
- Department of Medical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, People's Republic of China
| | - Hui Liu
- Department of Hematology, Beijing Hospital, National Center of Gerontology, Beijing, 1000730, People's Republic of China
| | - Hai-Chuan Zhu
- Institute of Biology and Medicine, College of Life and Health 20 Sciences, Wuhan University of Science and Technology, Hubei, 430081, People's Republic of China
| | - Chuan He
- Department of Chemistry, University of Chicago, Chicago, IL, 60637, USA
| | - Jian Lin
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Innovation Center for Genomics, Peking University, Beijing, 100871, People's Republic of China.
| | - Hong-Mei Jing
- Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, Beijing, 100191, People's Republic of China.
| |
Collapse
|
8
|
Cui XL, Nie J, Ku J, Dougherty U, West-Szymanski DC, Collin F, Ellison CK, Sieh L, Ning Y, Deng Z, Zhao CWT, Bergamaschi A, Pekow J, Wei J, Beadell AV, Zhang Z, Sharma G, Talwar R, Arensdorf P, Karpus J, Goel A, Bissonnette M, Zhang W, Levy S, He C. A human tissue map of 5-hydroxymethylcytosines exhibits tissue specificity through gene and enhancer modulation. Nat Commun 2020; 11:6161. [PMID: 33268789 PMCID: PMC7710742 DOI: 10.1038/s41467-020-20001-w] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 11/03/2020] [Indexed: 02/06/2023] Open
Abstract
DNA 5-hydroxymethylcytosine (5hmC) modification is known to be associated with gene transcription and frequently used as a mark to investigate dynamic DNA methylation conversion during mammalian development and in human diseases. However, the lack of genome-wide 5hmC profiles in different human tissue types impedes drawing generalized conclusions about how 5hmC is implicated in transcription activity and tissue specificity. To meet this need, we describe the development of a 5hmC tissue map by characterizing the genomic distributions of 5hmC in 19 human tissues derived from ten organ systems. Subsequent sequencing results enabled the identification of genome-wide 5hmC distributions that uniquely separates samples by tissue type. Further comparison of the 5hmC profiles with transcriptomes and histone modifications revealed that 5hmC is preferentially enriched on tissue-specific gene bodies and enhancers. Taken together, the results provide an extensive 5hmC map across diverse human tissue types that suggests a potential role of 5hmC in tissue-specific development; as well as a resource to facilitate future studies of DNA demethylation in pathogenesis and the development of 5hmC as biomarkers.
Collapse
Affiliation(s)
- Xiao-Long Cui
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, University of Chicago, Chicago, IL, USA
| | - Ji Nie
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, University of Chicago, Chicago, IL, USA
| | - Jeremy Ku
- Bluestar Genomics Inc., San Diego, CA, USA
| | | | - Diana C West-Szymanski
- Howard Hughes Medical Institute, University of Chicago, Chicago, IL, USA.,Department of Medicine, University of Chicago, Chicago, IL, USA
| | | | | | - Laura Sieh
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, University of Chicago, Chicago, IL, USA
| | | | - Zifeng Deng
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Carolyn W T Zhao
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, University of Chicago, Chicago, IL, USA
| | | | - Joel Pekow
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Jiangbo Wei
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, University of Chicago, Chicago, IL, USA
| | - Alana V Beadell
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, University of Chicago, Chicago, IL, USA
| | - Zhou Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Geeta Sharma
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | | | | | - Jason Karpus
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, University of Chicago, Chicago, IL, USA
| | - Ajay Goel
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | | | - Wei Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | | | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA. .,Howard Hughes Medical Institute, University of Chicago, Chicago, IL, USA.
| |
Collapse
|
9
|
Epigenome-wide association study reveals CpG sites related to COG of neuroblastoma. Biosci Rep 2020; 40:223850. [PMID: 32378698 PMCID: PMC7256671 DOI: 10.1042/bsr20200826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 04/29/2020] [Accepted: 05/04/2020] [Indexed: 11/30/2022] Open
Abstract
Background. Neuroblastoma (NB) is the most common extracranial solid tumor in infants and children. Its variable location and complex pathogenesis make NB hard for early diagnosis and risk classification. Methodology. We analyzed the methylation data of 236 samples from patients with NB in Therapeutically Applicable Research to Generate Effective Treatments (TARGET) database. Kaplan–Meier survival analysis was used for comparing overall survival of NB patients in different groups. Epigenome-wide association study (EWAS) was conducted to screen CpGs significantly associated with NB patients’ Children’s Oncology Group (COG). Logistic regression method was used for constructing a model to predict NB patients’ COG. Results. NB patients in low COG showed significantly superior prognosis than those in high COG. A total of seven CpG sites were found closely related to COG. Logistic regression model based on those CpGs showed superior performance in separating NB patients in different COGs. Conclusions. The present study highlights the important role of DNA methylation in NB development, which might provide evidence for treatment decisions for children NB.
Collapse
|
10
|
Applebaum MA, Barr EK, Karpus J, West-Szymanski DC, Oliva M, Sokol EA, Zhang S, Zhang Z, Zhang W, Chlenski A, Salwen HR, Wilkinson E, Dobratic M, Grossman RL, Godley LA, Stranger BE, He C, Cohn SL. 5-Hydroxymethylcytosine Profiles in Circulating Cell-Free DNA Associate with Disease Burden in Children with Neuroblastoma. Clin Cancer Res 2020; 26:1309-1317. [PMID: 31852832 PMCID: PMC7073281 DOI: 10.1158/1078-0432.ccr-19-2829] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 11/05/2019] [Accepted: 12/12/2019] [Indexed: 12/14/2022]
Abstract
PURPOSE 5-Hydroxymethylcytosine (5-hmC) is an epigenetic marker of open chromatin and active gene expression. We profiled 5-hmC with Nano-hmC-Seal technology using 10 ng of plasma-derived cell-free DNA (cfDNA) in blood samples from patients with neuroblastoma to determine its utility as a biomarker. EXPERIMENTAL DESIGN For the Discovery cohort, 100 5-hmC profiles were generated from 34 well children and 32 patients (27 high-risk, 2 intermediate-risk, and 3 low-risk) at various time points during the course of their disease. An independent Validation cohort encompassed 5-hmC cfDNA profiles (n = 29) generated from 21 patients (20 high-risk and 1 intermediate-risk). Metastatic burden was classified as high, moderate, low, or none per Curie metaiodobenzylguanidine scores and percentage of tumor cells in bone marrow. Genes with differential 5-hmC levels between samples according to metastatic burden were identified using DESeq2. RESULTS Hierarchical clustering using 5-hmC levels of 347 genes identified from the Discovery cohort defined four clusters of samples that were confirmed in the Validation cohort and corresponded to high, high-moderate, moderate, and low/no metastatic burden. Samples from patients with increased metastatic burden had increased 5-hmC deposition on genes in neuronal stem cell maintenance and epigenetic regulatory pathways. Further, 5-hmC cfDNA profiles generated with 1,242 neuronal pathway genes were associated with subsequent relapse in the cluster of patients with predominantly low or no metastatic burden (sensitivity 65%, specificity 75.6%). CONCLUSIONS cfDNA 5-hmC profiles in children with neuroblastoma correlate with metastatic burden and warrants development as a biomarker of treatment response and outcome.
Collapse
Affiliation(s)
- Mark A Applebaum
- Department of Pediatrics, University of Chicago, Chicago, Illinois.
| | - Erin K Barr
- Department of Pediatrics, Texas Tech University Health Sciences, Lubbock, Texas
| | - Jason Karpus
- Department of Chemistry, University of Chicago, Chicago, Illinois
| | | | - Meritxell Oliva
- Department of Medicine, University of Chicago, Chicago, Illinois
| | - Elizabeth A Sokol
- Department of Pediatrics, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois
| | - Sheng Zhang
- Department of Chemistry, University of Chicago, Chicago, Illinois
| | - Zhou Zhang
- Department of Preventive Medicine, Northwestern University, Chicago, Illinois
| | - Wei Zhang
- Department of Preventive Medicine, Northwestern University, Chicago, Illinois
| | | | - Helen R Salwen
- Department of Pediatrics, University of Chicago, Chicago, Illinois
| | - Emma Wilkinson
- Department of Pediatrics, University of Chicago, Chicago, Illinois
| | - Marija Dobratic
- Department of Pediatrics, University of Chicago, Chicago, Illinois
| | - Robert L Grossman
- Institute for Genomics and Systems Biology, Center for Translational Data Science, University of Chicago, Chicago, Illinois
| | - Lucy A Godley
- Department of Medicine, University of Chicago, Chicago, Illinois
| | | | - Chuan He
- Department of Chemistry, University of Chicago, Chicago, Illinois
- Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Susan L Cohn
- Department of Pediatrics, University of Chicago, Chicago, Illinois
| |
Collapse
|
11
|
Weiser DA, West-Szymanski DC, Fraint E, Weiner S, Rivas MA, Zhao CWT, He C, Applebaum MA. Progress toward liquid biopsies in pediatric solid tumors. Cancer Metastasis Rev 2020; 38:553-571. [PMID: 31836951 DOI: 10.1007/s10555-019-09825-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Pediatric solid tumors have long been known to shed tumor cells, DNA, RNA, and proteins into the blood. Recent technological advances have allowed for improved capture and analysis of these typically scant circulating materials. Efforts are ongoing to develop "liquid biopsy" assays as minimally invasive tools to address diagnostic, prognostic, and disease monitoring needs in childhood cancer care. Applying these highly sensitive technologies to serial liquid biopsies is expected to advance understanding of tumor biology, heterogeneity, and evolution over the course of therapy, thus opening new avenues for personalized therapy. In this review, we outline the latest technologies available for liquid biopsies and describe the methods, pitfalls, and benefits of the assays that are being developed for children with extracranial solid tumors. We discuss what has been learned in several of the most common pediatric solid tumors including neuroblastoma, sarcoma, Wilms tumor, and hepatoblastoma and highlight promising future directions for the field.
Collapse
Affiliation(s)
- Daniel A Weiser
- Department of Pediatrics, Albert Einstein College of Medicine and Children's Hospital at Montefiore, Bronx, NY, USA
| | | | - Ellen Fraint
- Department of Pediatrics, Albert Einstein College of Medicine and Children's Hospital at Montefiore, Bronx, NY, USA
| | - Shoshana Weiner
- Department of Pediatrics, Weill Cornell Medical Center, New York, NY, USA
| | - Marco A Rivas
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
| | - Carolyn W T Zhao
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Mark A Applebaum
- Department of Pediatrics, The University of Chicago, 900 E. 57th St., KCBD 5116, Chicago, IL, 60637, USA.
| |
Collapse
|
12
|
Zhang Z, Zhang W. Fragmentation patterns of circulating cell-free DNA demonstrate biomarker potential for human cancers. ACTA ACUST UNITED AC 2019; 3. [PMID: 31468030 DOI: 10.21037/biotarget.2019.08.02] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Zhou Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Wei Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA.,The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| |
Collapse
|