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Raj-Kumar PK, Lin X, Liu T, Sturtz LA, Gritsenko MA, Petyuk VA, Sagendorf TJ, Deyarmin B, Liu J, Praveen-Kumar A, Wang G, McDermott JE, Shukla AK, Moore RJ, Monroe ME, Webb-Robertson BJM, Hooke JA, Fantacone-Campbell L, Mostoller B, Kvecher L, Kane J, Melley J, Somiari S, Soon-Shiong P, Smith RD, Mural RJ, Rodland KD, Shriver CD, Kovatich AJ, Hu H. Proteogenomic characterization of difficult-to-treat breast cancer with tumor cells enriched through laser microdissection. Breast Cancer Res 2024; 26:76. [PMID: 38745208 PMCID: PMC11094977 DOI: 10.1186/s13058-024-01835-4] [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: 01/12/2024] [Accepted: 05/05/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Breast cancer (BC) is the most commonly diagnosed cancer and the leading cause of cancer death among women globally. Despite advances, there is considerable variation in clinical outcomes for patients with non-luminal A tumors, classified as difficult-to-treat breast cancers (DTBC). This study aims to delineate the proteogenomic landscape of DTBC tumors compared to luminal A (LumA) tumors. METHODS We retrospectively collected a total of 117 untreated primary breast tumor specimens, focusing on DTBC subtypes. Breast tumors were processed by laser microdissection (LMD) to enrich tumor cells. DNA, RNA, and protein were simultaneously extracted from each tumor preparation, followed by whole genome sequencing, paired-end RNA sequencing, global proteomics and phosphoproteomics. Differential feature analysis, pathway analysis and survival analysis were performed to better understand DTBC and investigate biomarkers. RESULTS We observed distinct variations in gene mutations, structural variations, and chromosomal alterations between DTBC and LumA breast tumors. DTBC tumors predominantly had more mutations in TP53, PLXNB3, Zinc finger genes, and fewer mutations in SDC2, CDH1, PIK3CA, SVIL, and PTEN. Notably, Cytoband 1q21, which contains numerous cell proliferation-related genes, was significantly amplified in the DTBC tumors. LMD successfully minimized stromal components and increased RNA-protein concordance, as evidenced by stromal score comparisons and proteomic analysis. Distinct DTBC and LumA-enriched clusters were observed by proteomic and phosphoproteomic clustering analysis, some with survival differences. Phosphoproteomics identified two distinct phosphoproteomic profiles for high relapse-risk and low relapse-risk basal-like tumors, involving several genes known to be associated with breast cancer oncogenesis and progression, including KIAA1522, DCK, FOXO3, MYO9B, ARID1A, EPRS, ZC3HAV1, and RBM14. Lastly, an integrated pathway analysis of multi-omics data highlighted a robust enrichment of proliferation pathways in DTBC tumors. CONCLUSIONS This study provides an integrated proteogenomic characterization of DTBC vs LumA with tumor cells enriched through laser microdissection. We identified many common features of DTBC tumors and the phosphopeptides that could serve as potential biomarkers for high/low relapse-risk basal-like BC and possibly guide treatment selections.
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Affiliation(s)
- Praveen-Kumar Raj-Kumar
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Xiaoying Lin
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Tao Liu
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Lori A Sturtz
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | | | | | | | - Brenda Deyarmin
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
| | - Jianfang Liu
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
| | | | - Guisong Wang
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | | | - Anil K Shukla
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ronald J Moore
- Pacific Northwest National Laboratory, Richland, WA, USA
| | | | | | - Jeffrey A Hooke
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | - Leigh Fantacone-Campbell
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | - Brad Mostoller
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
| | - Leonid Kvecher
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Jennifer Kane
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
| | - Jennifer Melley
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
| | - Stella Somiari
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
| | | | | | - Richard J Mural
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA
| | | | - Craig D Shriver
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
- Department of Surgery, Walter Reed National Military Medical Center, Bethesda, MD, USA.
| | - Albert J Kovatich
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA
| | - Hai Hu
- Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA, USA.
- Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
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Yan H, Huang J, Li Y, Zhao B. Sex disparities revealed by single-cell and bulk sequencing and their impacts on the efficacy of immunotherapy in esophageal cancer. Biol Sex Differ 2024; 15:22. [PMID: 38491510 PMCID: PMC10941500 DOI: 10.1186/s13293-024-00598-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 02/29/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND There is an ongoing debate on whether sex affects immune-suppressive tumor microenvironment and immunotherapy. Here, we explored the underlying molecular bases for sex dimorphisms and their impact on the efficacy of immunotherapy in esophageal cancer (EC). METHODS 2360 EC patients from phase 3 trials were pooled to compare overall survivals by calculating hazard ratios (HRs) and their 95% confidence intervals (CIs). Genomic data of 1425 samples were integrated to depict the genomic landscapes and antigenic features. We also examined the sex disparities based on single-cell RNA sequencing and T cell receptor-sequencing data from 105,145 immune cells in 60 patients. RESULTS Immunotherapy was associated with favorable outcomes in men (HR, 0.71; 95% CI, 0.65-0.79; P < 0.001), but not in women (HR, 0.98; 95% CI, 0.78-1.23; P = 0.84) (Pinteraction =0.02). The frequencies of 8 gene mutations, 12 single base substitutions signatures, and 131 reactome pathways were significantly different between male and female. Additionally, six subtypes of HLA-II antigens were enriched in women. Hence, we constructed and then validated a sex-related signature to better predict the outcomes of immunotherapy. Exhausted CD8+ T cells were highly infiltrated in men, while naïve CD8+ T cells were more common in women. Further examinations on multiple malignancies suggested exhausted CD8+ T cells were enriched in patients who responded to immunotherapy. CONCLUSIONS Our study delineated the robust genomic and cellular sex disparities in EC. Furthermore, male, rather than female, derived significantly benefits from immunotherapy. These results have implications for treatment decision-making and developing immunotherapy for personalized care. In the past several years, immunotherapy has gradually replaced the traditional chemotherapy as the standard treatment in esophageal cancer. It is well-established that immunological responses in male and female differ significantly. However, there is an ongoing debate on whether sex can impact the treatment outcomes in immunotherapy. In the present study, we systematically characterized the genomic and cellular landscapes of esophageal cancer, and revealed the significant differences between male and female patients. Furthermore, with over 2000 patients with esophageal cancer, we showed that only men can benefit from immunotherapy. In women, immunotherapy failed to show superior over chemotherapy. These results have implications for treatment decision-making and developing next-generation immunotherapy for personalized care.
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Affiliation(s)
- Huimeng Yan
- Second Affiliated Hospital, Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, 325035, China
- Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, 362000, China
| | - Jinyuan Huang
- Second Affiliated Hospital, Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, 325035, China
- Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, 362000, China
| | - Yingying Li
- Second Affiliated Hospital, Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, 325035, China
- Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, 362000, China
| | - Bin Zhao
- Second Affiliated Hospital, Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, 325035, China.
- Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, 362000, China.
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Chu J, Rong J, Feng X, Li H. ntsm: an alignment-free, ultra-low-coverage, sequencing technology agnostic, intraspecies sample comparison tool for sample swap detection. Gigascience 2024; 13:giae024. [PMID: 38832466 PMCID: PMC11148594 DOI: 10.1093/gigascience/giae024] [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: 11/01/2023] [Revised: 02/13/2024] [Accepted: 04/30/2024] [Indexed: 06/05/2024] Open
Abstract
BACKGROUND Due to human error, sample swapping in large cohort studies with heterogeneous data types (e.g., mix of Oxford Nanopore Technologies, Pacific Bioscience, Illumina data, etc.) remains a common issue plaguing large-scale studies. At present, all sample swapping detection methods require costly and unnecessary (e.g., if data are only used for genome assembly) alignment, positional sorting, and indexing of the data in order to compare similarly. As studies include more samples and new sequencing data types, robust quality control tools will become increasingly important. FINDINGS The similarity between samples can be determined using indexed k-mer sequence variants. To increase statistical power, we use coverage information on variant sites, calculating similarity using a likelihood ratio-based test. Per sample error rate, and coverage bias (i.e., missing sites) can also be estimated with this information, which can be used to determine if a spatially indexed principal component analysis (PCA)-based prescreening method can be used, which can greatly speed up analysis by preventing exhaustive all-to-all comparisons. CONCLUSIONS Because this tool processes raw data, is faster than alignment, and can be used on very low-coverage data, it can save an immense degree of computational resources in standard quality control (QC) pipelines. It is robust enough to be used on different sequencing data types, important in studies that leverage the strengths of different sequencing technologies. In addition to its primary use case of sample swap detection, this method also provides information useful in QC, such as error rate and coverage bias, as well as population-level PCA ancestry analysis visualization.
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Affiliation(s)
- Justin Chu
- Dana-Farber Cancer Institute, Department of Data Sciences, Boston, MA 02215, USA
- Harvard Medical School, Department of Biomedical Informatics, Boston, MA 02115, USA
| | - Jiazhen Rong
- Genomics and Computational Biology Graduate Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Xiaowen Feng
- Dana-Farber Cancer Institute, Department of Data Sciences, Boston, MA 02215, USA
- Harvard Medical School, Department of Biomedical Informatics, Boston, MA 02115, USA
| | - Heng Li
- Dana-Farber Cancer Institute, Department of Data Sciences, Boston, MA 02215, USA
- Harvard Medical School, Department of Biomedical Informatics, Boston, MA 02115, USA
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Chao A, Wu RC, Lin CY, Lee LY, Tsai CL, Lee YS, Wang CJ. Targeted next-generation sequencing for the detection of cancer-associated somatic mutations in adenomyosis. J OBSTET GYNAECOL 2023; 43:2161352. [PMID: 36708516 DOI: 10.1080/01443615.2022.2161352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Adenomyosis is a condition characterised by the invasion of endometrial tissues into the uterine myometrium, the molecular pathogenesis of which remains incompletely elucidated. Lesion profiling with next-generation sequencing (NGS) can lead to the identification of previously unanticipated causative genes and the detection of therapeutically actionable genetic changes. Using an NGS panel that included 275 cancer susceptibility genes, this study examined the occurrence and frequency of somatic mutations in adenomyotic tissue specimens collected from 17 women. Extracted DNA was enriched using targeted formalin-fixed paraffin-embedded tissue cores prior to the identification of lesion-specific variants. The results revealed that KRAS and AT-rich interactive domain 1A (ARID1A) were the two most frequently mutated genes (mutation frequencies: 24% and 12%, respectively). Notably, endometrial atypical hyperplasia did not involve adenomyotic areas. We also identified, for the first time, two potentially pathogenic mutations in the F-box/WD repeat-containing protein 7 (FBXW7) and cohesin subunit SA-2 (STAG2) genes. These findings indicate that mutations in the KRAS, ARID1A, FBXW7 and STAG2 genes may play a critical role in the pathogenesis of adenomyosis. Additional studies are needed to assess whether the utilisation of oncogenic driver mutations can inform the surveillance of patients with adenomyosis who had not undergone hysterectomy.Impact statementWhat is already known on this subject? Although somatic point mutations in the KRAS oncogene have been recently detected in adenomyosis, the molecular underpinnings of this condition remains incompletely elucidated. Lesion profiling with next-generation sequencing (NGS) can lead to the identification of previously unanticipated causative genes and the detection of therapeutically actionable genetic changes.What do the results of this study add? The results of NGS revealed that KRAS and AT-rich interactive domain 1A (ARID1A) were the two most frequently mutated genes (mutation frequencies: 24% and 12%, respectively). We also identified, for the first time, two potentially pathogenic mutations in the F-box/WD repeat-containing protein 7 (FBXW7) and cohesin subunit SA-2 (STAG2) genes.What are the implications of these findings for clinical practice and/or further research? The utilisation of oncogenic driver mutations has the potential to inform the surveillance of patients with adenomyosis who had not undergone hysterectomy.
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Affiliation(s)
- Angel Chao
- Department of Obstetrics and Gynaecology, Linkou Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taoyuan, Taiwan.,Gynaecologic Cancer Research Centre, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Ren-Chin Wu
- Department of Pathology, Linkou Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Chiao-Yun Lin
- Department of Obstetrics and Gynaecology, Linkou Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taoyuan, Taiwan.,Gynaecologic Cancer Research Centre, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Lee-Yu Lee
- Department of Pathology, Linkou Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Chia-Lung Tsai
- Genomic Medicine Research Core Laboratory, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yun-Shien Lee
- Department of Biotechnology, Ming Chuan University, Taoyuan, Taiwan
| | - Chin-Jung Wang
- Department of Obstetrics and Gynaecology, Linkou Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taoyuan, Taiwan.,Gynaecologic Cancer Research Centre, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
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High frequency of colorectal neoplasia in patients with sporadic adenomas or adenocarcinomas of the papilla of Vater: The same adenoma-carcinoma sequence? Dig Liver Dis 2022; 55:679-684. [PMID: 36411191 DOI: 10.1016/j.dld.2022.10.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/30/2022] [Accepted: 10/14/2022] [Indexed: 11/19/2022]
Abstract
BACKGROUND Data on the frequency of colorectal neoplasia in sporadic ampullary tumors remains scarce. METHODS We retrospectively reviewed 135 patients undergoing endoscopic ampullectomy from January 2018 to July 2021, and identified 95 patients with sporadic ampullary adenoma who underwent total colonoscopy. Colonoscopy findings were compared with 380 asymptomatic controls using the chi-squared test. Whole-exome sequencing (WES) was performed on one patient with synchronous adenomas of the ampulla of Vater and ascending colon. RESULTS Colorectal polyps were present in 60% of Cases vs. 34.7% of Controls (P = 0.001), advanced adenoma in 20% vs. 5.5%, and adenocarcinoma in 4.2% vs. 0.8%. Cases tended to have larger polyps than Controls (P<0.001), while there was no difference in polyp location and histology between the two groups. The odds ratio of all the colorectal lesions, advanced colorectal adenoma and adenocarcinoma in Cases was 1.7, 4.2, and 4, respectively. WES in one patient revealed that both of ampullary adenoma and colonic adenoma shared somatic ABCB1 mutation. CONCLUSIONS The frequency of colorectal polyps or neoplasia was significantly higher in Cases than Controls. We proposed that ampullary neoplasia is analogous to colon lesions and warrants total colonoscopy screening in patients diagnosed with ampullary tumors.
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Integrated cohort of esophageal squamous cell cancer reveals genomic features underlying clinical characteristics. Nat Commun 2022; 13:5268. [PMID: 36071046 PMCID: PMC9452532 DOI: 10.1038/s41467-022-32962-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 08/25/2022] [Indexed: 11/08/2022] Open
Abstract
Esophageal squamous cell cancer (ESCC) is the major pathologic type of esophageal cancer in Asian population. To systematically evaluate the mutational features underlying clinical characteristics, we establish the integrated dataset of ESCC-META that consists of 1930 ESCC genomes from 33 datasets. The data process pipelines lead to well homogeneity of this integrated cohort for further analysis. We identified 11 mutational signatures in ESCC, some of which are related to clinical features, and firstly detect the significant mutated hotspots in TGFBR2 and IRF2BPL. We screen the survival related mutational features and found some genes had different prognostic impacts between early and late stage, such as PIK3CA and NFE2L2. Based on the results, an applicable approach of mutational score is proposed and validated to predict prognosis in ESCC. As an open-sourced, quality-controlled and updating mutational landscape, the ESCC-META dataset could facilitate further genomic and translational study in this field.
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Su F, Liu M, Zhang W, Tang M, Zhang J, Li H, Zou L, Zhang R, Liu Y, Li L, Ma J, Zhang Y, Chen M, Xiao F. Bacillus Calmette–Guérin Treatment Changes the Tumor Microenvironment of Non-Muscle-Invasive Bladder Cancer. Front Oncol 2022; 12:842182. [PMID: 35311085 PMCID: PMC8930202 DOI: 10.3389/fonc.2022.842182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 02/03/2022] [Indexed: 12/24/2022] Open
Abstract
Background Bacillus Calmette–Guérin (BCG) is currently the most effective intravesical therapy for non-muscle-invasive bladder cancer (NMIBC) as it can prevent disease recurrence and progression and lower mortality. However, the response rates to BCG vary widely and are dependent on a multitude of factors. Methods We performed a systematic discovery by analyzing the whole exome sequence, expression profile, and immune repertoire sequence of treatment-naive and 5-year time-serial relapsed tumors from 24 NMIBC patients. Results BCG therapy showed bidirectional effects on tumor evolution and immune checkpoint landscape, along with a significant reduction of the percentage of neoantigen burden. In addition, a remarkable proportion of subclonal mutations were unique to the matched pre- or post-treatment tumors, suggesting the presence of BCG-induced and/or spatial heterogeneity. In the relapsed tumors, we identified and validated a shift in the mutational signatures in which mutations associated with aristolochic acid (AA) exposure were enriched, implying AA may be associated with tumor recurrence. Enhanced expressions of immune checkpoint regulation genes were found in the relapsed tumors, suggesting that the combination of immune checkpoint with BCG treatment may be an effective strategy to treat NMIBC. TCR sequencing revealed treatment-associated changes in the T-cell repertoire in the primary and relapsed tumors. Conclusion Our results provide insight into the genomic and immune dynamics of tumor evolution with BCG treatment, suggest new mechanisms of BCG resistance, and inform the development of clinically relevant biomarkers and trials of potential immune checkpoint inhibitor combination therapies.
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Affiliation(s)
- Fei Su
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Ming Liu
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Wei Zhang
- Department of Pathology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Min Tang
- Department of Oncology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Jinsong Zhang
- Department of Pathology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Hexin Li
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Lihui Zou
- The Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Rui Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Yudong Liu
- The Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Lin Li
- Department of Oncology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Jie Ma
- Center for Biotherapy, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- State Key Lab of Molecular Oncology, National Cancer Center, Chinese Academy of Medical Sciences Cancer Hospital & Peking Union Medical College, Beijing, China
| | - Yaqun Zhang
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- *Correspondence: Yaqun Zhang, ; Meng Chen, ; Fei Xiao,
| | - Meng Chen
- National Cancer Data Center, National Cancer Center, Chinese Academy of Medical Sciences Cancer Hospital & Peking Union Medical College, Beijing, China
- *Correspondence: Yaqun Zhang, ; Meng Chen, ; Fei Xiao,
| | - Fei Xiao
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- The Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- *Correspondence: Yaqun Zhang, ; Meng Chen, ; Fei Xiao,
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Tsang KY, Chan TCH, Yeung MCW, Wong TK, Lau WT, Mak CM. Validation of amplicon-based next generation sequencing panel for second-tier test in newborn screening for inborn errors of metabolism. J LAB MED 2021. [DOI: 10.1515/labmed-2021-0115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Objectives
Next generation sequencing (NGS) technology has allowed cost-effective massive parallel DNA sequencing. To evaluate the utility of NGS for newborn screening (NBS) of inborn errors of metabolism (IEM), a custom panel was designed to target 87 disease-related genes. The pilot study was primarily proposed for second-tier testing under the NBSIEM program in Hong Kong.
Methods
The validation of the panel was performed with two reference genomes and an external quality assurance (EQA) sample. Sequencing libraries were synthesized with amplicon-based approach. The libraries were pooled, spiked-in with 2% PhiX DNA as technical control, for 16-plex sequencing runs. Sequenced reads were analyzed using a commercially available pipeline.
Results
The average target region coverage was 208× and the fraction of region with target depth ≥20× was 95.7%, with a sensitivity of 91.2%. There were 85 out of 87 genes with acceptable coverage, and EQA result was satisfactory. The turnaround time from DNA extraction to completion of variant calling and quality control (QC) procedures was 2.5 days.
Conclusions
The NGS approach with the amplicon-based panel has been validated for analytical performance and is suitable for second-tier NBSIEM test.
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Affiliation(s)
- Kwok Yeung Tsang
- Newborn Screening for Inborn Errors of Metabolism Laboratory, Hong Kong Children's Hospital , Hong Kong SAR , P.R. China
- Department of Pathology, Division of Chemical Pathology , Hong Kong Children’s Hospital , Hong Kong SAR , P.R. China
| | - Toby Chun Hei Chan
- Newborn Screening for Inborn Errors of Metabolism Laboratory, Hong Kong Children's Hospital , Hong Kong SAR , P.R. China
- Department of Pathology, Division of Chemical Pathology , Hong Kong Children’s Hospital , Hong Kong SAR , P.R. China
| | - Matthew Chun Wing Yeung
- Newborn Screening for Inborn Errors of Metabolism Laboratory, Hong Kong Children's Hospital , Hong Kong SAR , P.R. China
- Department of Pathology, Division of Chemical Pathology , Hong Kong Children’s Hospital , Hong Kong SAR , P.R. China
| | - Tsz Ki Wong
- Newborn Screening for Inborn Errors of Metabolism Laboratory, Hong Kong Children's Hospital , Hong Kong SAR , P.R. China
| | - Wan Ting Lau
- Newborn Screening for Inborn Errors of Metabolism Laboratory, Hong Kong Children's Hospital , Hong Kong SAR , P.R. China
| | - Chloe Miu Mak
- Newborn Screening for Inborn Errors of Metabolism Laboratory, Hong Kong Children's Hospital , Hong Kong SAR , P.R. China
- Department of Pathology, Division of Chemical Pathology , Hong Kong Children’s Hospital , Hong Kong SAR , P.R. China
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Genomic characterization of co-existing neoplasia and carcinoma lesions reveals distinct evolutionary paths of gallbladder cancer. Nat Commun 2021; 12:4753. [PMID: 34362903 PMCID: PMC8346570 DOI: 10.1038/s41467-021-25012-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 07/16/2021] [Indexed: 12/30/2022] Open
Abstract
Gallbladder carcinoma is the most common cancer of the biliary tract with dismal survival largely due to delayed diagnosis. Biliary tract intraepithelial neoplasia (BilIN) is the common benign tumor that is suspected to be precancerous lesions. However, the genetic and evolutionary relationships between BilIN and carcinoma remain unclear. Here we perform whole-exome sequencing of coexisting low-grade BilIN (adenoma), high-grade BilIN, and carcinoma lesions, and normal tissues from the same patients. We identify aging as a major factor contributing to accumulated mutations and a critical role of CTNNB1 mutations in these tumors. We reveal two distinct carcinoma evolutionary paths: carcinoma can either diverge earlier and evolve more independently or form through the classic adenoma/dysplasia-carcinoma sequence model. Our analysis suggests that extensive loss-of-heterozygosity and mutation events in the initial stage tend to result in a cancerous niche, leading to the subsequent BilIN-independent path. These results reframes our understanding of tumor transformation and the evolutionary trajectory of carcinogenesis in the gallbladder, laying a foundation for the early diagnosis and effective treatment of gallbladder cancer. The progression from biliary tract intraepithelial neoplasia (BilIN) to gallbladder carcinoma (GBC) remains unclear. Here the authors use genomics to analyze coexisting GBC lesions, low-grade and high-grade BilINs, revealing two distinct evolutionary paths for GBC development.
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10
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Banerjee S, Zhang X, Kuang S, Wang J, Li L, Fan G, Luo Y, Sun S, Han P, Wu Q, Yang S, Ji X, Li Y, Deng L, Tian X, Wang Z, Zhang Y, Wu K, Zhu S, Bolund L, Yang H, Xu X, Liu J, Lu Y, Liu X. Comparative analysis of clonal evolution among patients with right- and left-sided colon and rectal cancer. iScience 2021; 24:102718. [PMID: 34258553 PMCID: PMC8254024 DOI: 10.1016/j.isci.2021.102718] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/21/2020] [Accepted: 06/09/2021] [Indexed: 12/15/2022] Open
Abstract
Tumor multiregion sequencing reveals intratumor heterogeneity (ITH) and clonal evolution playing a key role in tumor progression and metastases. Large-scale high-depth multiregional sequencing of colorectal cancer, comparative analysis among patients with right-sided colon cancer (RCC), left-sided colon cancer (LCC), and rectal cancer (RC), as well as the study of lymph node metastasis (LN) with extranodal tumor deposits (ENTDs) from evolutionary perspective remain weakly explored. Here, we recruited 68 patients with RCC (18), LCC (20), and RC (30). We performed high-depth whole-exome sequencing of 206 tumor regions including 176 primary tumors, 19 LN, and 11 ENTD samples. Our results showed ITH with a Darwinian pattern of evolution and the evolution pattern of LCC and RC was more complex and divergent than RCC. Genetic and evolutionary evidences found that both LN and ENTD originated from different clones. Moreover, ENTD was a distinct entity from LN and evolved later.
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Affiliation(s)
- Santasree Banerjee
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.,BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Xianxiang Zhang
- Department of Gastroenterology, General Surgery Center, The Affiliated Hospital of Qingdao University, Qingdao 266555, China
| | - Shan Kuang
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Jigang Wang
- Department of Pathology, The Affiliated Hospital of Qingdao University, Qingdao 266555, China
| | - Lei Li
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China.,School of Future Technology, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.,BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Yonglun Luo
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.,BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China.,Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark
| | - Shuai Sun
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.,BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Peng Han
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Qingyao Wu
- Department of Gastroenterology, General Surgery Center, The Affiliated Hospital of Qingdao University, Qingdao 266555, China
| | - Shujian Yang
- Department of Gastroenterology, General Surgery Center, The Affiliated Hospital of Qingdao University, Qingdao 266555, China
| | - Xiaobin Ji
- Department of Pathology, The Affiliated Hospital of Qingdao University, Qingdao 266555, China
| | - Yong Li
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Li Deng
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Xiaofen Tian
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China.,MGI, BGI-Shenzhen, Shenzhen 518083, China
| | - Zhiwei Wang
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.,BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Yue Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Kui Wu
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Shida Zhu
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Lars Bolund
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.,BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China.,Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark.,Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518083, China.,James D. Watson Institute of Genome Sciences, Hangzhou 310058, Zhejiang, China
| | - Xun Xu
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.,BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Junnian Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.,BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Yun Lu
- Department of Gastroenterology, General Surgery Center, The Affiliated Hospital of Qingdao University, Qingdao 266555, China.,Shandong Key Laboratory of Digital Medicine and Computer Assisted Surgery, Qingdao University, Qingdao, China
| | - Xin Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.,BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
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11
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Analysis of the genomic landscape of yolk sac tumors reveals mechanisms of evolution and chemoresistance. Nat Commun 2021; 12:3579. [PMID: 34117242 PMCID: PMC8196104 DOI: 10.1038/s41467-021-23681-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 05/11/2021] [Indexed: 12/22/2022] Open
Abstract
Yolk sac tumors (YSTs) are a major histological subtype of malignant ovarian germ cell tumors with a relatively poor prognosis. The molecular basis of this disease has not been thoroughly characterized at the genomic level. Here we perform whole-exome and RNA sequencing on 41 clinical tumor samples from 30 YST patients, with distinct responses to cisplatin-based chemotherapy. We show that microsatellite instability status and mutational signatures are informative of chemoresistance. We identify somatic driver candidates, including significantly mutated genes KRAS and KIT and copy-number alteration drivers, including deleted ARID1A and PARK2, and amplified ZNF217, CDKN1B, and KRAS. YSTs have very infrequent TP53 mutations, whereas the tumors from patients with abnormal gonadal development contain both KRAS and TP53 mutations. We further reveal a role of OVOL2 overexpression in YST resistance to cisplatin. This study lays a critical foundation for understanding key molecular aberrations in YSTs and developing related therapeutic strategies.
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12
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Distinct mutational backgrounds and clonal architectures implicated prognostic discrepancies in small-cell carcinomas of the esophagus and lung. Cell Death Dis 2021; 12:472. [PMID: 33980813 PMCID: PMC8115141 DOI: 10.1038/s41419-021-03754-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 11/08/2022]
Abstract
Small-cell carcinoma of the esophagus (SCCE) is a rare and aggressive cancer. Although several consistent genomic changes were observed previously between SCCE and small-cell lung cancer (SCLC), detailed mutational landscapes revealing discrepancies in genetic underpinnings of tumorigenesis between these two cancers are scarce, and little attention has been paid to answer whether these genetic alterations were related to the prognosis. Herein by performing whole-exome sequencing of 48 SCCE and 64 SCLC tumor samples, respectively we have shown that the number of driver mutations in SCCE was significantly lower than in SCLC (p = 0.0042). In SCCE, 46% of recurrent driver mutations were clonal, which occurred at an early stage during tumorigenesis, while 16 driver mutations were found clonal in SCLC. NOTCH1/3, PIK3CA, and ATM were specifically clonal in SCCE, while TP53 was clonal in SCLC. The total number of clonal mutations differed between two cancers and presented lower in SCCE compared to SCLC (p = 0.0036). Moreover, overall survival (OS) was shorter in patients with higher numbers of clonal mutations for both cancers. In summary, SCCE showed distinct mutational background and clonal architecture compared with SCLC. Organ-specific clonal events revealed different molecular mechanisms underlying tumorigenesis, tumor development, patients’ prognosis, and possible variations in therapeutic outcomes to candidate treatments.
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13
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Thompson AS, Saba N, McReynolds LJ, Munir S, Ahmed P, Sajjad S, Jones K, Yeager M, Donovan FX, Chandrasekharappa SC, Alter BP, Savage SA, Rehman S. The causes of Fanconi anemia in South Asia and the Middle East: A case series and review of the literature. Mol Genet Genomic Med 2021; 9:e1693. [PMID: 33960719 PMCID: PMC8372062 DOI: 10.1002/mgg3.1693] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/16/2021] [Accepted: 04/09/2021] [Indexed: 02/06/2023] Open
Abstract
Background Fanconi anemia (FA) is an inherited bone marrow failure syndrome associated with characteristic dysmorphology primarily caused by biallelic pathogenic germline variants in any of 22 different DNA repair genes. There are limited data on the specific molecular causes of FA in different ethnic groups. Methods We performed exome sequencing and copy number variant analyses on 19 patients with FA from 17 families undergoing hematopoietic cell transplantation evaluation in Pakistan. The scientific literature was reviewed, and we curated germline variants reported in patients with FA from South Asia and the Middle East. Results The genetic causes of FA were identified in 14 of the 17 families: seven FANCA, two FANCC, one FANCF, two FANCG, and two FANCL. Homozygous and compound heterozygous variants were present in 12 and two families, respectively. Nine families carried variants previously reported as pathogenic, including two families with the South Asian FANCL founder variant. We also identified five novel likely deleterious variants in FANCA, FANCF, and FANCG in affected patients. Conclusions Our study supports the importance of determining the genomic landscape of FA in diverse populations, in order to improve understanding of FA etiology and assist in the counseling of families.
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Affiliation(s)
- Ashley S Thompson
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Nusrat Saba
- Institute of Biomedical and Genetic Engineering, Islamabad, Pakistan
| | - Lisa J McReynolds
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Saeeda Munir
- Institute of Biomedical and Genetic Engineering, Islamabad, Pakistan
| | - Parvez Ahmed
- Quaid-i-Azam International Hospital, Islamabad, Pakistan
| | - Sumaira Sajjad
- Institute of Biomedical and Genetic Engineering, Islamabad, Pakistan
| | - Kristine Jones
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, 20850, USA
| | - Meredith Yeager
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, 20850, USA
| | - Frank X Donovan
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Settara C Chandrasekharappa
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Blanche P Alter
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Sharon A Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Sadia Rehman
- Institute of Biomedical and Genetic Engineering, Islamabad, Pakistan
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14
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Sex-based differences in the activation of peripheral blood monocytes in early Parkinson disease. NPJ PARKINSONS DISEASE 2021; 7:36. [PMID: 33850148 PMCID: PMC8044127 DOI: 10.1038/s41531-021-00180-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 03/17/2021] [Indexed: 12/12/2022]
Abstract
Increasing evidence supports the role of brain and systemic inflammation in the etiology of Parkinson disease (PD). We used gene expression profiling to examine the activation state of peripheral blood monocytes in 18 patients with early, untreated PD and 16 healthy control (HC) subjects. Monocytes were isolated by negative selection, and gene expression studied by RNA-seq and gene set enrichment analysis. A computational model that incorporated case/control status, sex, and the interaction between case/control status and sex was utilized. We found that there was a striking effect of sex on monocyte gene expression. There was inflammatory activation of monocytes in females with PD, with enrichment of gene sets associated with interferon gamma stimulation. In males, the activation patterns were more heterogeneous. These data point to the importance of systemic monocyte activation in PD, and the importance of studies which examine the differential effects of sex on pathophysiology of the disease.
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15
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Bai J, Shi J, Li C, Wang S, Zhang T, Hua X, Zhu B, Koka H, Wu HH, Song L, Wang D, Wang M, Zhou W, Ballew BJ, Zhu B, Hicks B, Mirabello L, Parry DM, Zhai Y, Li M, Du J, Wang J, Zhang S, Liu Q, Zhao P, Gui S, Goldstein AM, Zhang Y, Yang XR. Whole genome sequencing of skull-base chordoma reveals genomic alterations associated with recurrence and chordoma-specific survival. Nat Commun 2021; 12:757. [PMID: 33536423 PMCID: PMC7859411 DOI: 10.1038/s41467-021-21026-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 01/06/2021] [Indexed: 02/06/2023] Open
Abstract
Chordoma is a rare bone tumor with an unknown etiology and high recurrence rate. Here we conduct whole genome sequencing of 80 skull-base chordomas and identify PBRM1, a SWI/SNF (SWItch/Sucrose Non-Fermentable) complex subunit gene, as a significantly mutated driver gene. Genomic alterations in PBRM1 (12.5%) and homozygous deletions of the CDKN2A/2B locus are the most prevalent events. The combination of PBRM1 alterations and the chromosome 22q deletion, which involves another SWI/SNF gene (SMARCB1), shows strong associations with poor chordoma-specific survival (Hazard ratio [HR] = 10.55, 95% confidence interval [CI] = 2.81-39.64, p = 0.001) and recurrence-free survival (HR = 4.30, 95% CI = 2.34-7.91, p = 2.77 × 10-6). Despite the low mutation rate, extensive somatic copy number alterations frequently occur, most of which are clonal and showed highly concordant profiles between paired primary and recurrence/metastasis samples, indicating their importance in chordoma initiation. In this work, our findings provide important biological and clinical insights into skull-base chordoma.
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Affiliation(s)
- Jiwei Bai
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Chuzhong Li
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
- Brain Tumor Center, Beijing Institute for Brain Disorders, Beijing, China
| | - Shuai Wang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Xing Hua
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Hela Koka
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Ho-Hsiang Wu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Lei Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Difei Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Mingyi Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Weiyin Zhou
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Bari J Ballew
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Belynda Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Dilys M Parry
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Yixuan Zhai
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Mingxuan Li
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Jiang Du
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
- Brain Tumor Center, Beijing Institute for Brain Disorders, Beijing, China
| | - Junmei Wang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
- Brain Tumor Center, Beijing Institute for Brain Disorders, Beijing, China
| | - Shuheng Zhang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
- Department of Neurosurgery, Anshan Central Hospital, Anshan, China
| | - Qian Liu
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Peng Zhao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Songbai Gui
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Alisa M Goldstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Yazhuo Zhang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.
- China National Clinical Research Center for Neurological Diseases, Beijing, China.
- Brain Tumor Center, Beijing Institute for Brain Disorders, Beijing, China.
| | - Xiaohong R Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
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16
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Modeling performance of sample collection sites using whole exome sequencing metrics. Biotechniques 2020; 69:420-426. [PMID: 33103912 DOI: 10.2144/btn-2020-0086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Although next-generation sequencing assays are routinely carried out using samples from cancer trials, the sequencing data are not always of the required quality. There is a need to evaluate the performance of tissue collection sites and provide feedback about the quality of next-generation sequencing data. This study used a modeling approach based on whole exome sequencing quality control (QC) metrics to evaluate the relative performance of sites participating in the Bristol Myers Squibb Immuno-Oncology clinical trials sample collection. We identified several events for the sample swap. Overall, most sites performed well and few showed poor performance. These findings can increase awareness of sample failure and improve the quality of samples.
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17
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Javed N, Farjoun Y, Fennell TJ, Epstein CB, Bernstein BE, Shoresh N. Detecting sample swaps in diverse NGS data types using linkage disequilibrium. Nat Commun 2020; 11:3697. [PMID: 32728101 PMCID: PMC7391710 DOI: 10.1038/s41467-020-17453-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 06/29/2020] [Indexed: 11/24/2022] Open
Abstract
As the number of genomics datasets grows rapidly, sample mislabeling has become a high stakes issue. We present CrosscheckFingerprints (Crosscheck), a tool for quantifying sample-relatedness and detecting incorrectly paired sequencing datasets from different donors. Crosscheck outperforms similar methods and is effective even when data are sparse or from different assays. Application of Crosscheck to 8851 ENCODE ChIP-, RNA-, and DNase-seq datasets enabled us to identify and correct dozens of mislabeled samples and ambiguous metadata annotations, representing ~1% of ENCODE datasets. Parallelized analysis in clinical genomics can lead to sample or data mislabelling, and could have serious downstream consequences. Here the authors present a tool to quantify sample genetic relatedness and detect such mistakes, and apply it to thousands of datasets from the ENCODE consortium.
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Affiliation(s)
- Nauman Javed
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Yossi Farjoun
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Tim J Fennell
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | | | - Bradley E Bernstein
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Noam Shoresh
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
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18
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Chun H, Kim S. BAMixChecker: an automated checkup tool for matched sample pairs in NGS cohort. Bioinformatics 2020; 35:4806-4808. [PMID: 31197312 PMCID: PMC6853765 DOI: 10.1093/bioinformatics/btz479] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 05/28/2019] [Accepted: 06/05/2019] [Indexed: 11/13/2022] Open
Abstract
SUMMARY Mislabeling in the process of next generation sequencing is a frequent problem that can cause an entire genomic analysis to fail, and a regular cohort-level checkup is needed to ensure that it has not occurred. We developed a new, automated tool (BAMixChecker) that accurately detects sample mismatches from a given BAM file cohort with minimal user intervention. BAMixChecker uses a flexible, data-specific set of single-nucleotide polymorphisms and detects orphan (unpaired) and swapped (mispaired) samples based on genotype-concordance score and entropy-based file name analysis. BAMixChecker shows ∼100% accuracy in real WES, RNA-Seq and targeted sequencing data cohorts, even for small panels (<50 genes). BAMixChecker provides an HTML-style report that graphically outlines the sample matching status in tables and heatmaps, with which users can quickly inspect any mismatch events. AVAILABILITY AND IMPLEMENTATION BAMixChecker is available at https://github.com/heinc1010/BAMixChecker. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Hein Chun
- Department of Biomedical Systems Informatics, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Sangwoo Kim
- Department of Biomedical Systems Informatics, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, South Korea
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19
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The genomic and epigenomic evolutionary history of papillary renal cell carcinomas. Nat Commun 2020; 11:3096. [PMID: 32555180 PMCID: PMC7303129 DOI: 10.1038/s41467-020-16546-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 05/10/2020] [Indexed: 12/12/2022] Open
Abstract
Intratumor heterogeneity (ITH) and tumor evolution have been well described for clear cell renal cell carcinomas (ccRCC), but they are less studied for other kidney cancer subtypes. Here we investigate ITH and clonal evolution of papillary renal cell carcinoma (pRCC) and rarer kidney cancer subtypes, integrating whole-genome sequencing and DNA methylation data. In 29 tumors, up to 10 samples from the center to the periphery of each tumor, and metastatic samples in 2 cases, enable phylogenetic analysis of spatial features of clonal expansion, which shows congruent patterns of genomic and epigenomic evolution. In contrast to previous studies of ccRCC, in pRCC, driver gene mutations and most arm-level somatic copy number alterations (SCNAs) are clonal. These findings suggest that a single biopsy would be sufficient to identify the important genetic drivers and that targeting large-scale SCNAs may improve pRCC treatment, which is currently poor. While type 1 pRCC displays near absence of structural variants (SVs), the more aggressive type 2 pRCC and the rarer subtypes have numerous SVs, which should be pursued for prognostic significance.
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20
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He X, Chen S, Li R, Han X, He Z, Yuan D, Zhang S, Duan X, Niu B. Comprehensive fundamental somatic variant calling and quality management strategies for human cancer genomes. Brief Bioinform 2020; 22:5854402. [PMID: 32510555 DOI: 10.1093/bib/bbaa083] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/19/2020] [Accepted: 04/21/2020] [Indexed: 12/21/2022] Open
Abstract
Next-generation sequencing (NGS) technology has revolutionised human cancer research, particularly via detection of genomic variants with its ultra-high-throughput sequencing and increasing affordability. However, the inundation of rich cancer genomics data has resulted in significant challenges in its exploration and translation into biological insights. One of the difficulties in cancer genome sequencing is software selection. Currently, multiple tools are widely used to process NGS data in four stages: raw sequence data pre-processing and quality control (QC), sequence alignment, variant calling and annotation and visualisation. However, the differences between these NGS tools, including their installation, merits, drawbacks and application, have not been fully appreciated. Therefore, a systematic review of the functionality and performance of NGS tools is required to provide cancer researchers with guidance on software and strategy selection. Another challenge is the multidimensional QC of sequencing data because QC can not only report varied sequence data characteristics but also reveal deviations in diverse features and is essential for a meaningful and successful study. However, monitoring of QC metrics in specific steps including alignment and variant calling is neglected in certain pipelines such as the 'Best Practices Workflows' in GATK. In this review, we investigated the most widely used software for the fundamental analysis and QC of cancer genome sequencing data and provided instructions for selecting the most appropriate software and pipelines to ensure precise and efficient conclusions. We further discussed the prospects and new research directions for cancer genomics.
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A human lung tumor microenvironment interactome identifies clinically relevant cell-type cross-talk. Genome Biol 2020; 21:107. [PMID: 32381040 PMCID: PMC7206807 DOI: 10.1186/s13059-020-02019-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 04/15/2020] [Indexed: 12/11/2022] Open
Abstract
Background Tumors comprise a complex microenvironment of interacting malignant and stromal cell types. Much of our understanding of the tumor microenvironment comes from in vitro studies isolating the interactions between malignant cells and a single stromal cell type, often along a single pathway. Result To develop a deeper understanding of the interactions between cells within human lung tumors, we perform RNA-seq profiling of flow-sorted malignant cells, endothelial cells, immune cells, fibroblasts, and bulk cells from freshly resected human primary non-small-cell lung tumors. We map the cell-specific differential expression of prognostically associated secreted factors and cell surface genes, and computationally reconstruct cross-talk between these cell types to generate a novel resource called the Lung Tumor Microenvironment Interactome (LTMI). Using this resource, we identify and validate a prognostically unfavorable influence of Gremlin-1 production by fibroblasts on proliferation of malignant lung adenocarcinoma cells. We also find a prognostically favorable association between infiltration of mast cells and less aggressive tumor cell behavior. Conclusion These results illustrate the utility of the LTMI as a resource for generating hypotheses concerning tumor-microenvironment interactions that may have prognostic and therapeutic relevance. Supplementary information Supplementary information accompanies this paper at 10.1186/s13059-020-02019-x.
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Chang H, Sasson A, Srinivasan S, Golhar R, Greenawalt DM, Geese WJ, Green G, Zerba K, Kirov S, Szustakowski J. Bioinformatic Methods and Bridging of Assay Results for Reliable Tumor Mutational Burden Assessment in Non-Small-Cell Lung Cancer. Mol Diagn Ther 2020; 23:507-520. [PMID: 31250328 PMCID: PMC6675777 DOI: 10.1007/s40291-019-00408-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Introduction Tumor mutational burden (TMB) has emerged as a clinically relevant biomarker that may be associated with immune checkpoint inhibitor efficacy. Standardization of TMB measurement is essential for implementing diagnostic tools to guide treatment. Objective Here we describe the in-depth evaluation of bioinformatic TMB analysis by whole exome sequencing (WES) in formalin-fixed, paraffin-embedded samples from a phase III clinical trial. Methods In the CheckMate 026 clinical trial, TMB was retrospectively assessed in 312 patients with non-small-cell lung cancer (58% of the intent-to-treat population) who received first-line nivolumab treatment or standard-of-care chemotherapy. We examined the sensitivity of TMB assessment to bioinformatic filtering methods and assessed concordance between TMB data derived by WES and the FoundationOne® CDx assay. Results TMB scores comprising synonymous, indel, frameshift, and nonsense mutations (all mutations) were 3.1-fold higher than data including missense mutations only, but values were highly correlated (Spearman’s r = 0.99). Scores from CheckMate 026 samples including missense mutations only were similar to those generated from data in The Cancer Genome Atlas, but those including all mutations were generally higher. Using databases for germline subtraction (instead of matched controls) showed a trend for race-dependent increases in TMB scores. WES and FoundationOne CDx outputs were highly correlated (Spearman’s r = 0.90). Conclusions Parameter variation can impact TMB calculations, highlighting the need for standardization. Encouragingly, differences between assays could be accounted for by empirical calibration, suggesting that reliable TMB assessment across assays, platforms, and centers is achievable.
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Affiliation(s)
- Han Chang
- Translational Medicine, Bristol-Myers Squibb, Princeton, NJ, 08648, USA
| | - Ariella Sasson
- Translational Medicine, Bristol-Myers Squibb, Princeton, NJ, 08648, USA
| | - Sujaya Srinivasan
- Translational Medicine, Bristol-Myers Squibb, Princeton, NJ, 08648, USA
| | - Ryan Golhar
- Translational Medicine, Bristol-Myers Squibb, Princeton, NJ, 08648, USA
| | | | - William J Geese
- Translational Medicine, Bristol-Myers Squibb, Princeton, NJ, 08648, USA
| | - George Green
- Translational Medicine, Bristol-Myers Squibb, Princeton, NJ, 08648, USA
| | - Kim Zerba
- Global Biometric Sciences, Bristol-Myers Squibb, Princeton, NJ, USA
| | - Stefan Kirov
- Translational Medicine, Bristol-Myers Squibb, Princeton, NJ, 08648, USA
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Whole transcriptome analysis and validation of metabolic pathways in subcutaneous adipose tissues during FGF21-induced weight loss in non-human primates. Sci Rep 2020; 10:7287. [PMID: 32350364 PMCID: PMC7190698 DOI: 10.1038/s41598-020-64170-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 04/09/2020] [Indexed: 01/01/2023] Open
Abstract
Fibroblast growth factor 21 (FGF21) induces weight loss in mouse, monkey, and human studies. In mice, FGF21 is thought to cause weight loss by stimulating thermogenesis, but whether FGF21 increases energy expenditure (EE) in primates is unclear. Here, we explore the transcriptional response and gene networks active in adipose tissue of rhesus macaques following FGF21-induced weight loss. Genes related to thermogenesis responded inconsistently to FGF21 treatment and weight loss. However, expression of gene modules involved in triglyceride (TG) synthesis and adipogenesis decreased, and this was associated with greater weight loss. Conversely, expression of innate immune cell markers was increased post-treatment and was associated with greater weight loss. A lipogenesis gene module associated with weight loss was evaluated by testing the function of member genes in mice. Overexpression of NRG4 reduced weight gain in diet-induced obese mice, while overexpression of ANGPTL8 resulted in elevated TG levels in lean mice. These observations provide evidence for a shifting balance of lipid storage and metabolism due to FGF21-induced weight loss in the non-human primate model, and do not fully recapitulate increased EE seen in rodent and in vitro studies. These discrepancies may reflect inter-species differences or complex interplay of FGF21 activity and counter-regulatory mechanisms.
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Comprehensive transcriptome profiling of Taiwanese colorectal cancer implicates an ethnic basis for pathogenesis. Sci Rep 2020; 10:4526. [PMID: 32161294 PMCID: PMC7066141 DOI: 10.1038/s41598-020-61273-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 02/19/2020] [Indexed: 02/07/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most commonly diagnosed cancers worldwide. While both genetic and environmental factors have been linked to the incidence and mortality associated with CRC, an ethnic aspect of its etiology has also emerged. Since previous large-scale cancer genomics studies are mostly based on samples of European ancestry, the patterns of clinical events and associated mechanisms in other minority ethnic patients suffering from CRC are largely unexplored. We collected 104 paired and adjacent normal tissue and CRC tumor samples from Taiwanese patients and employed an integrated approach - paired expression profiles of mRNAs and microRNAs (miRNAs) combined with transcriptome-wide network analyses - to catalog the molecular signatures of this regional cohort. On the basis of this dataset, which is the largest ever reported for this type of systems analysis, we made the following key discoveries: (1) In comparison to the The Cancer Genome Atlas (TCGA) data, the Taiwanese CRC tumors show similar perturbations in expressed genes but a distinct enrichment in metastasis-associated pathways. (2) Recurrent as well as novel CRC-associated gene fusions were identified based on the sequencing data. (3) Cancer subtype classification using existing tools reveals a comparable distribution of tumor subtypes between Taiwanese cohort and TCGA datasets; however, this similarity in molecular attributes did not translate into the predicted subtype-related clinical outcomes (i.e., death event). (4) To further elucidate the molecular basis of CRC prognosis, we developed a new stratification strategy based on miRNA-mRNA-associated subtyping (MMAS) and consequently showed that repressed WNT signaling activity is associated with poor prognosis in Taiwanese CRC. In summary, our findings of distinct, hitherto unreported biosignatures underscore the heterogeneity of CRC tumorigenesis, support our hypothesis of an ethnic basis of disease, and provide prospects for translational medicine.
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Hellmann MD, Callahan MK, Awad MM, Calvo E, Ascierto PA, Atmaca A, Rizvi NA, Hirsch FR, Selvaggi G, Szustakowski JD, Sasson A, Golhar R, Vitazka P, Chang H, Geese WJ, Antonia SJ. Tumor Mutational Burden and Efficacy of Nivolumab Monotherapy and in Combination with Ipilimumab in Small-Cell Lung Cancer. Cancer Cell 2018; 33:853-861.e4. [PMID: 29731394 PMCID: PMC6750707 DOI: 10.1016/j.ccell.2018.04.001] [Citation(s) in RCA: 600] [Impact Index Per Article: 100.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 02/12/2018] [Accepted: 04/02/2018] [Indexed: 12/13/2022]
Abstract
Durable responses and encouraging survival have been demonstrated with immune checkpoint inhibitors in small-cell lung cancer (SCLC), but predictive markers are unknown. We used whole exome sequencing to evaluate the impact of tumor mutational burden on efficacy of nivolumab monotherapy or combined with ipilimumab in patients with SCLC from the nonrandomized or randomized cohorts of CheckMate 032. Patients received nivolumab (3 mg/kg every 2 weeks) or nivolumab plus ipilimumab (1 mg/kg plus 3 mg/kg every 3 weeks for four cycles, followed by nivolumab 3 mg/kg every 2 weeks). Efficacy of nivolumab ± ipilimumab was enhanced in patients with high tumor mutational burden. Nivolumab plus ipilimumab appeared to provide a greater clinical benefit than nivolumab monotherapy in the high tumor mutational burden tertile.
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Affiliation(s)
- Matthew D Hellmann
- Thoracic Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, Weill Cornell Medical College, and Parker Center for Cancer Immunotherapy, 885 2nd Avenue, New York, NY 10017, USA.
| | - Margaret K Callahan
- Thoracic Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, Weill Cornell Medical College, and Parker Center for Cancer Immunotherapy, 885 2nd Avenue, New York, NY 10017, USA
| | - Mark M Awad
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Emiliano Calvo
- START Madrid, Centro Integral Oncológico Clara Campal, Medical Oncology Division, Hospital Universitario Madrid Norte Sanchinarro, Madrid 28050, Spain
| | - Paolo A Ascierto
- Unit of Melanoma, Cancer Immunotherapy and Innovative Therapy, Istituto Nazionale Tumori Fondazione G. Pascale, Naples 80131, Italy
| | - Akin Atmaca
- Department of Hematology and Oncology, Krankenhaus Nordwest, UCT-University Cancer Center, Frankfurt am Main 60488, Germany
| | - Naiyer A Rizvi
- Division of Hematology and Oncology, Columbia University Medical Center, New York, NY 10032, USA
| | - Fred R Hirsch
- Department of Medicine, Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Giovanni Selvaggi
- Clinical Development, Bristol-Myers Squibb, Princeton, NJ 08648, USA
| | | | - Ariella Sasson
- Translational Medicine, Bristol-Myers Squibb, Princeton, NJ 08648, USA
| | - Ryan Golhar
- Translational Medicine, Bristol-Myers Squibb, Princeton, NJ 08648, USA
| | - Patrik Vitazka
- Translational Medicine, Bristol-Myers Squibb, Princeton, NJ 08648, USA
| | - Han Chang
- Translational Medicine, Bristol-Myers Squibb, Princeton, NJ 08648, USA
| | - William J Geese
- Translational Medicine, Bristol-Myers Squibb, Princeton, NJ 08648, USA
| | - Scott J Antonia
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
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Montalban-Bravo G, Takahashi K, Patel K, Wang F, Xingzhi S, Nogueras GM, Huang X, Pierola AA, Jabbour E, Colla S, Gañan-Gomez I, Borthakur G, Daver N, Estrov Z, Kadia T, Pemmaraju N, Ravandi F, Bueso-Ramos C, Chamseddine A, Konopleva M, Zhang J, Kantarjian H, Futreal A, Garcia-Manero G. Impact of the number of mutations in survival and response outcomes to hypomethylating agents in patients with myelodysplastic syndromes or myelodysplastic/myeloproliferative neoplasms. Oncotarget 2018. [PMID: 29515765 PMCID: PMC5839396 DOI: 10.18632/oncotarget.23882] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The prognostic and predictive value of sequencing analysis in myelodysplastic syndromes (MDS) has not been fully integrated into clinical practice. We performed whole exome sequencing (WES) of bone marrow samples from 83 patients with MDS and 31 with MDS/MPN identifying 218 driver mutations in 31 genes in 98 (86%) patients. A total of 65 (57%) patients received therapy with hypomethylating agents. By univariate analysis, mutations in BCOR, STAG2, TP53 and SF3B1 significantly influenced survival. Increased number of mutations (≥ 3), but not clonal heterogeneity, predicted for shorter survival and LFS. Presence of 3 or more mutations also predicted for lower likelihood of response (26 vs 50%, p = 0.055), and shorter response duration (3.6 vs 26.5 months, p = 0.022). By multivariate analysis, TP53 mutations (HR 3.1, CI 1.3–7.5, p = 0.011) and number of mutations (≥ 3) (HR 2.5, CI 1.3–4.8, p = 0.005) predicted for shorter survival. A novel prognostic model integrating this mutation data with IPSS-R separated patients into three categories with median survival of not reached, 29 months and 12 months respectively (p < 0.001) and increased stratification potential, compared to IPSS-R, in patients with high/very-high IPSS-R. This model was validated in a separate cohort of 413 patients with untreated MDS. Although the use of WES did not provide significant more information than that obtained with targeted sequencing, our findings indicate that increased number of mutations is an independent prognostic factor in MDS and that mutation data can add value to clinical prognostic models.
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Affiliation(s)
| | - Koichi Takahashi
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.,Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Keyur Patel
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Feng Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Song Xingzhi
- Applied Cancer Science Institute, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Graciela M Nogueras
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Xuelin Huang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ana Alfonso Pierola
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Elias Jabbour
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Simona Colla
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Irene Gañan-Gomez
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Gautham Borthakur
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Naval Daver
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Zeev Estrov
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Tapan Kadia
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Naveen Pemmaraju
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Farhad Ravandi
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Carlos Bueso-Ramos
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ali Chamseddine
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Marina Konopleva
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jianhua Zhang
- Applied Cancer Science Institute, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Hagop Kantarjian
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Guillermo Garcia-Manero
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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27
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Glusman G, Mauldin DE, Hood LE, Robinson M. Ultrafast Comparison of Personal Genomes via Precomputed Genome Fingerprints. Front Genet 2017; 8:136. [PMID: 29018478 PMCID: PMC5623000 DOI: 10.3389/fgene.2017.00136] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 09/12/2017] [Indexed: 01/01/2023] Open
Abstract
We present an ultrafast method for comparing personal genomes. We transform the standard genome representation (lists of variants relative to a reference) into “genome fingerprints” via locality sensitive hashing. The resulting genome fingerprints can be meaningfully compared even when the input data were obtained using different sequencing technologies, processed using different pipelines, represented in different data formats and relative to different reference versions. Furthermore, genome fingerprints are robust to up to 30% missing data. Because of their reduced size, computation on the genome fingerprints is fast and requires little memory. For example, we could compute all-against-all pairwise comparisons among the 2504 genomes in the 1000 Genomes data set in 67 s at high quality (21 μs per comparison, on a single processor), and achieved a lower quality approximation in just 11 s. Efficient computation enables scaling up a variety of important genome analyses, including quantifying relatedness, recognizing duplicative sequenced genomes in a set, population reconstruction, and many others. The original genome representation cannot be reconstructed from its fingerprint, effectively decoupling genome comparison from genome interpretation; the method thus has significant implications for privacy-preserving genome analytics.
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Affiliation(s)
| | | | - Leroy E Hood
- Institute for Systems Biology, Seattle, WA, United States
| | - Max Robinson
- Institute for Systems Biology, Seattle, WA, United States
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