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Kumar R, Awasthi S, Pradhan D, Kumar R, Goel H, Singh J, Haider I, Deo SVS, Kumar C, Srivastava A, Bhatnagar A, Kumar R, Lakshmi S, Augustine P, Ranjan A, Chopra A, Gogia A, Batra A, Mathur S, Rath GK, Kaur T, Dhaliwal RS, Mathew A, Agrawal U, Hussain S, Tanwar P. Somatic mutational landscape across Indian breast cancer cases by whole exome sequencing. Sci Rep 2024; 14:18679. [PMID: 39134585 PMCID: PMC11319672 DOI: 10.1038/s41598-024-65148-4] [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: 11/07/2023] [Accepted: 06/17/2024] [Indexed: 08/15/2024] Open
Abstract
Breast cancer (BC) has emerged as the most common malignancy among females. The genomic profile of BC is diverse in nature and complex due to heterogeneity among various geographically different ethnic groups. The primary objective of this study was to carry out a comprehensive mutational analysis of Indian BC cases by performing whole exome sequencing. The cohort included patients with a median age of 48 years. TTN, TP53, MUC16, SYNE1, and OBSCN were the frequently altered genes found in our cohort. The PIK3CA and KLC3 genes are driver genes implicated in various cellular functions and cargo transportation through microtubules, respectively. Except for CCDC168 and PIK3CA, several gene pairings were found to be significantly linked with co-occurrence. Irrespective of their hormonal receptor status, RTK/RAS was observed with frequently altered signaling pathways. Further analysis of the mutational signature revealed that SBS13, SBS6, and SBS29 were mainly observed in our cohort. This study supplements the discovery of diagnostic biomarkers and provides new therapeutic options for the improved management of BC.
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Affiliation(s)
- Rahul Kumar
- Dr. B. R. A.-Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Supriya Awasthi
- Dr. B. R. A.-Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | | | - Rakesh Kumar
- Dr. B. R. A.-Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Harsh Goel
- Dr. B. R. A.-Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Jay Singh
- Dr. B. R. A.-Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Imran Haider
- Dr. B. R. A.-Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - S V S Deo
- Dr. B. R. A.-Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Chitresh Kumar
- Dr. B. R. A.-Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Anurag Srivastava
- Department of General Surgery, All India Institute of Medical Sciences, New Delhi, India
| | - Amar Bhatnagar
- Vardhman Mahavir Medical College and Safdarjung Hospital, New Delhi, India
| | - Rakesh Kumar
- Vardhman Mahavir Medical College and Safdarjung Hospital, New Delhi, India
| | - S Lakshmi
- Division of Cancer Research, Regional Cancer Centre, Thiruvananthapuram, Kerala, India
| | - Paul Augustine
- Division of Surgical Services, Regional Cancer Centre, Thiruvananthapuram, Kerala, India
| | - Amar Ranjan
- Dr. B. R. A.-Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Anita Chopra
- Dr. B. R. A.-Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Ajay Gogia
- Dr. B. R. A.-Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Atul Batra
- Dr. B. R. A.-Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Sandeep Mathur
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Goura Kishor Rath
- Dr. B. R. A.-Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Tanvir Kaur
- Division of Non-Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - R S Dhaliwal
- Division of Non-Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - Aleyamma Mathew
- Division of Cancer Epidemiology and Biostatistics, Regional Cancer Centre, Thiruvananthapuram, Kerala, India
| | - Usha Agrawal
- ICMR-National Institute of Pathology, New Delhi, India
| | - Showket Hussain
- Division of Molecular Oncology, National Institute of Cancer Prevention and Research, Noida, India
| | - Pranay Tanwar
- Dr. B. R. A.-Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India.
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2
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Gomez GA, Udayakumar A, Pourteymoor S, Dennis G, Xing W, Mohan S. Evaluation of Potential Roles of Zinc Finger Homeobox 3 (Zfhx3) Expressed in Chondrocytes and Osteoblasts on Skeletal Growth in Mice. Calcif Tissue Int 2024:10.1007/s00223-024-01265-6. [PMID: 39085428 DOI: 10.1007/s00223-024-01265-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 07/20/2024] [Indexed: 08/02/2024]
Abstract
Bone formation is tightly modulated by genetically encoded molecular proteins that interact to regulate cellular differentiation and secretion of bony matrix. Many transcription factors are known to coordinate these events by controlling gene transcription within networks. However, not all factors involved are known. Here, we identified a novel function for Zinc Finger Homeobox 3 (Zfhx3), a gene encoding a transcription factor, as a regulator of bone metabolism. We knocked out Zfhx3 conditionally in mice in either chondrocytes or osteoblasts and characterized their bones by micro-CT in 12-week-old mice. We observed a negative effect in linear bone growth in both knockout mice but reduced bone mass only in mice with Zfhx3 deleted in osteoblasts. Loss of Zfhx3 expression in osteoblasts affected trabecular bone mass in femurs and vertebrae in both sexes but influenced cortical bone volume fraction only in females. Moreover, transcriptional analysis of femoral bones in osteoblast Zfhx3 conditional knockout mice revealed a reduced expression of osteoblast genes, and histological evaluation of trabecular bones suggests that Zfhx3 causes changes in bone formation and not resorption. The loss of Zfhx3 causes reductions in trabecular bone area and osteoid volume, but no changes in the expression of osteoclast differentiation markers or number of TRAP stained osteoclasts. These studies introduce Zfhx3 as a relevant factor toward understanding gene regulatory networks that control bone formation and development of peak bone mass.
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Affiliation(s)
- Gustavo A Gomez
- Musculoskeletal Disease Center, VA Loma Linda Healthcare System, 11201 Benton Street, Loma Linda, CA, 92357, USA
| | - Anakha Udayakumar
- Musculoskeletal Disease Center, VA Loma Linda Healthcare System, 11201 Benton Street, Loma Linda, CA, 92357, USA
| | - Sheila Pourteymoor
- Musculoskeletal Disease Center, VA Loma Linda Healthcare System, 11201 Benton Street, Loma Linda, CA, 92357, USA
| | - Garrett Dennis
- Musculoskeletal Disease Center, VA Loma Linda Healthcare System, 11201 Benton Street, Loma Linda, CA, 92357, USA
| | - Weirong Xing
- Musculoskeletal Disease Center, VA Loma Linda Healthcare System, 11201 Benton Street, Loma Linda, CA, 92357, USA
| | - Subburaman Mohan
- Musculoskeletal Disease Center, VA Loma Linda Healthcare System, 11201 Benton Street, Loma Linda, CA, 92357, USA.
- Departments of Medicine, Biochemistry and Orthopedic Surgery, Loma Linda University, Loma Linda, CA, 92354, USA.
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3
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Hu Q, Yin J, Zhao S, Wang Y, Shi R, Yan K, Huang S. ZFHX3 acts as a tumor suppressor in prostate cancer by targeting FTO-mediated m 6A demethylation. Cell Death Discov 2024; 10:284. [PMID: 38871709 DOI: 10.1038/s41420-024-02060-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/31/2024] [Accepted: 06/05/2024] [Indexed: 06/15/2024] Open
Abstract
Zinc-finger homeobox 3 (ZFHX3, also known as ATBF1) suppresses prostatic tumorigenesis. ZFHX3 is frequently found to have numerous deletions in human prostate cancer (PCa). However, the underlying molecular function of ZFHX3 during prostatic tumorigenesis is not well understood. N6-methyladenosine (m6A) modification in RNA plays a critical role in the development of cancers; however, the relationship between ZFHX3 and m6A modification is largely unknown in PCa. In this study, we found that ZFHX3 knockdown decreased total m6A levels through enhancing the transcriptional activity of FTO in PCa cells. Importantly, FTO inhibition suppressed cell proliferation and rescued the promoting function of ZFHX3 knockdown on cell proliferation. In vivo, we verified that FTO was upregulated and ZFHX3 was decreased in PCa patients and that a high level of ZFHX3 is indispensable for low FTO expression and is correlated with better patient survival. Through transcriptome sequencing and MeRIP sequencing, we revealed that E2F2 and CDKN2C were the direct targets of FTO-mediated m6A modification and ZFXH3 was required for the regulation of FTO on E2F2 and CDKN2C expression. Unexpectedly, we uncovered that ZFHX3 expression was in return regulated by FTO in an m6A-dependent way. These findings establish a novel crosstalk mechanism between ZFHX3 and FTO in prostatic tumorigenesis.
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Affiliation(s)
- Qingxia Hu
- School of Clinical and Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
- Shandong Provincial Hospital of Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Junling Yin
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Sijie Zhao
- School of Clinical and Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Yibo Wang
- Shandong Provincial Hospital of Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Ruxue Shi
- School of Clinical and Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Keqiang Yan
- Department of Urology, Qilu Hospital of Shandong University, Jinan, 250012, Shandong, China.
| | - Shuhong Huang
- School of Clinical and Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China.
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China.
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4
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Tang S, Chen F, Zhang J, Chang F, Lv Z, Li K, Li S, Hu Y, Yeh S. LncRNA-SERB promotes vasculogenic mimicry (VM) formation and tumor metastasis in renal cell carcinoma. J Biol Chem 2024; 300:107297. [PMID: 38641065 PMCID: PMC11126803 DOI: 10.1016/j.jbc.2024.107297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 03/03/2024] [Accepted: 03/31/2024] [Indexed: 04/21/2024] Open
Abstract
A growing body of evidence shows that vasculogenic mimicry (VM) is closely related to the invasion and metastasis of many tumor cells. Although the estrogen receptor (ER) can promote initiation and progression of renal cell carcinoma (RCC), how the downstream biomolecules are involved, and the detailed mechanisms of how ER expression is elevated in RCC remain to be further elucidated. Here, we discovered that long noncoding RNA (LncRNA)-SERB is highly expressed in tumor cells of RCC patients. We used multiple RCC cells and an in vivo mouse model for our study, and results indicated that LncRNA-SERB could boost RCC VM formation and cell invasion in vitro and in vivo. Although a previous report showed that ERβ can affect the VM formation in RCC, it is unclear which factor could upregulate ERβ. This is the first study to show LncRNA-SERB can be the upstream regulator of ERβ to control RCC progression. Mechanistically, LncRNA-SERB may increase ERβ via binding to the promoter area, and ERβ functions through transcriptional regulation of zinc finger E-box binding homeobox 1 (ZEB1) to regulate VM formation. These results suggest that LncRNA-SERB promotes RCC cell VM formation and invasion by upregulating the ERβ/ZEB1 axis and that therapeutic targeting of this newly identified pathway may better inhibit RCC progression.
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MESH Headings
- Carcinoma, Renal Cell/genetics
- Carcinoma, Renal Cell/metabolism
- Carcinoma, Renal Cell/pathology
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- Humans
- Kidney Neoplasms/pathology
- Kidney Neoplasms/metabolism
- Kidney Neoplasms/genetics
- Animals
- Mice
- Neovascularization, Pathologic/metabolism
- Neovascularization, Pathologic/genetics
- Neovascularization, Pathologic/pathology
- Gene Expression Regulation, Neoplastic
- Estrogen Receptor beta/metabolism
- Estrogen Receptor beta/genetics
- Cell Line, Tumor
- Zinc Finger E-box-Binding Homeobox 1/metabolism
- Zinc Finger E-box-Binding Homeobox 1/genetics
- Neoplasm Metastasis
- Mice, Nude
- Male
- Female
- Neoplasm Invasiveness
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Affiliation(s)
- Shuai Tang
- College of Medicine, Nankai University, Tianjin, China; Department of Urology, Nankai University Affinity The Third Central Hospital, Tianjin, China; Department of Urology, The Third Central Hospital of Tianjin, Tianjin, China; Departments of Urology, Pathology, and The Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, New York, USA
| | - Fangmin Chen
- College of Medicine, Nankai University, Tianjin, China; Department of Urology, Nankai University Affinity The Third Central Hospital, Tianjin, China; Department of Urology, The Third Central Hospital of Tianjin, Tianjin, China.
| | - Jianghui Zhang
- Department of Urology, Nankai University Affinity The Third Central Hospital, Tianjin, China; Department of Urology, The Third Central Hospital of Tianjin, Tianjin, China
| | - Fan Chang
- Department of Urology, Nankai University Affinity The Third Central Hospital, Tianjin, China; Department of Urology, The Third Central Hospital of Tianjin, Tianjin, China
| | - Zheng Lv
- Department of Urology, Nankai University Affinity The Third Central Hospital, Tianjin, China; Department of Urology, The Third Central Hospital of Tianjin, Tianjin, China
| | - Kai Li
- Department of Urology, Nankai University Affinity The Third Central Hospital, Tianjin, China; Department of Urology, The Third Central Hospital of Tianjin, Tianjin, China
| | - Song Li
- Department of Urology, Nankai University Affinity The Third Central Hospital, Tianjin, China; Department of Urology, The Third Central Hospital of Tianjin, Tianjin, China
| | - Yixi Hu
- Departments of Urology, Pathology, and The Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, New York, USA
| | - Shuyuan Yeh
- Departments of Urology, Pathology, and The Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, New York, USA; The Sex Hormone Research Center and Department of Urology, China Medical University/Hospital, Taichung, Taiwan.
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5
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Krull JE, Wenzl K, Hopper MA, Manske MK, Sarangi V, Maurer MJ, Larson MC, Mondello P, Yang Z, Novak JP, Serres M, Whitaker KR, Villasboas Bisneto JC, Habermann TM, Witzig TE, Link BK, Rimsza LM, King RL, Ansell SM, Cerhan JR, Novak AJ. Follicular lymphoma B cells exhibit heterogeneous transcriptional states with associated somatic alterations and tumor microenvironments. Cell Rep Med 2024; 5:101443. [PMID: 38428430 PMCID: PMC10983045 DOI: 10.1016/j.xcrm.2024.101443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 08/14/2023] [Accepted: 02/05/2024] [Indexed: 03/03/2024]
Abstract
Follicular lymphoma (FL) is an indolent non-Hodgkin lymphoma of germinal center origin, which presents with significant biologic and clinical heterogeneity. Using RNA-seq on B cells sorted from 87 FL biopsies, combined with machine-learning approaches, we identify 3 transcriptional states that divide the biological ontology of FL B cells into inflamed, proliferative, and chromatin-modifying states, with relationship to prior GC B cell phenotypes. When integrated with whole-exome sequencing and immune profiling, we find that each state was associated with a combination of mutations in chromatin modifiers, copy-number alterations to TNFAIP3, and T follicular helper cells (Tfh) cell interactions, or primarily by a microenvironment rich in activated T cells. Altogether, these data define FL B cell transcriptional states across a large cohort of patients, contribute to our understanding of FL heterogeneity at the tumor cell level, and provide a foundation for guiding therapeutic intervention.
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Affiliation(s)
| | - Kerstin Wenzl
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | | | | | | | - Matthew J Maurer
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Melissa C Larson
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | | | - ZhiZhang Yang
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | | | | | | | | | | | | | - Brian K Link
- Division of Hematology, Oncology, and Blood & Marrow Transplantation, University of Iowa, Iowa City, IA, USA
| | - Lisa M Rimsza
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Scottsdale, AZ, USA
| | - Rebecca L King
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - James R Cerhan
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Anne J Novak
- Division of Hematology, Mayo Clinic, Rochester, MN, USA.
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Chen Q, Guo H, Jiang H, Hu Z, Yang X, Yuan Z, Gao Y, Zhang G, Bai Y. S100A2 induces epithelial-mesenchymal transition and metastasis in pancreatic cancer by coordinating transforming growth factor β signaling in SMAD4-dependent manner. Cell Death Discov 2023; 9:356. [PMID: 37758734 PMCID: PMC10533899 DOI: 10.1038/s41420-023-01661-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/08/2023] [Accepted: 09/20/2023] [Indexed: 09/29/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive tumor and is associated with a poor prognosis. Treatment strategies for PDAC are largely ineffective primarily because of delay in its diagnosis and limited efficacy of systematic treatment. S100A2 is associated with the proliferation, migration, and differentiation of several tumors; however, its effects on PDAC and the associated molecular mechanisms remain to be explored. We studied the mechanisms underlying the effect of S100A2 on epithelial-mesenchymal transition (EMT) and metastasis in PDAC cells. We found that the level of S100A2 remarkably increased and was associated with poor PDAC prognosis. The overexpression of S100A2 in PANC-1 cells also induced EMT, in addition to increasing the invasion and migration of PDAC cells, whereas the knockdown of S100A2 markedly inhibited cell metastasis. Furthermore, S100A2 was found to enhance metastatic abilities in vivo. The overexpression of S100A2 increased SMAD4 expression, whereas the knockdown of S100A2 reduced SMAD4 expression. SMAD4 overexpression could effectively rescue the effects of S100A2 knockdown on EMT. S100A2 mechanistically activated the transforming growth factor (TGF)-β/Smad2/3 signaling pathway, upregulated SMAD4 expression, induced EMT, and increased PANC-1 cell metastasis. In conclusion, the S100A2/SMAD4 axis modulates EMT to accelerate PDAC development. Our results supplement and enrich the understanding of the pathogenesis underlying PDAC and provide a new theoretical basis and strategy targeting S100A2 for the diagnosis and treatment of PDAC.
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Affiliation(s)
- Qinbo Chen
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, 325000, Wenzhou, China
| | - Hangcheng Guo
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, 325000, Wenzhou, China
| | - Haojie Jiang
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, 325000, Wenzhou, China
| | - Zujian Hu
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, 325000, Wenzhou, China
| | - Xuejia Yang
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, 325000, Wenzhou, China
| | - Ziwei Yuan
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, 325000, Wenzhou, China
| | - Yuanyuan Gao
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, 325000, Wenzhou, China
| | - Ge Zhang
- Department of Orthopedics, The First Affiliated Hospital of Southwest Medical University, 646000, Luzhou, China
| | - Yongheng Bai
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, 325000, Wenzhou, China.
- National Key Clinical Specialty (General Surgery), The First Affiliated Hospital of Wenzhou Medical University, 325000, Wenzhou, China.
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7
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Cai R, Zhu H, Liu Y, Sha H, Peng W, Yin R, Zhou G, Fang Y. To be, or not to be: the dilemma of immunotherapy for non-small cell lung cancer harboring various driver mutations. J Cancer Res Clin Oncol 2023; 149:10027-10040. [PMID: 37261523 PMCID: PMC10423141 DOI: 10.1007/s00432-023-04919-4] [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: 03/23/2023] [Accepted: 05/23/2023] [Indexed: 06/02/2023]
Abstract
INTRODUCTION Lung cancer is one of primary cancer type with high incidence and mortality, non-small cell lung cancer (NSCLC) is the most common type of lung cncer. For advanced lung cancer, traditional chemotherapy and targeted therapy become difficult to solve the dilemma of further progress. In recent years, with the clinical application of immunotherapy, the therapeutic strategy of lung cancer has changed dramatically. At present, immunotherapy has shown conspicuous efficacy in NSCLC patients with high expression of programmed death-ligand 1 (PD-L1) and high tumor mutational burden (TMB). The discovery of driver mutations brings delightful hope for targeted cancer therapy. However, it remains controversial whether immunotherapy can be used in NSCLC patients with these specific driver mutations. METHOD This article summarized the latest research progresses of immunotherapy in advanced NSCLC. We paid close attention to the relevance of various driver mutations and immunotherapy in NSCLC patients, and summarized the predictive effects of several driver mutations and immunotherapy. RESULTS The mutations of KRAS, KRAS+TP53, EPHA (especially EPHA5), ZFHX3, ZFHX3+TP53, NOTCH, BRAF and LRP1B+FAT3 have potential to be used as biomarkers to predict the positive effectiveness of immunotherapy. ZFHX3, ZFHX3+TP53, STKII/LKB1+KEAP1+SMARCA4+PBRM1 mutations in LUAD patients get more positive effect in immunotherapy. While the mutations of EGFR, KEAP1, STKII/LKB1+KRAS, EML4-ALK, MET exon 14 skipping mutation, PBRM1, STKII/LKB1+KEAP1+SMARCA4+PBRM1, ERBB2, PIK3CA and RET often indicate poor benefit from immunotherapy. CONCLUSION Many gene mutations have been shown to be associated with immunotherapy efficacy. Gene mutations should be combined with PD-L1, TMB, etc. to predict the effect of immunotherapy.
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Affiliation(s)
- Ruoxue Cai
- Department of Oncology, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Baiziting 42, Nanjing, 210009, People's Republic of China
| | - Hongyu Zhu
- Department of Thoracic Surgery, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, 210009, People's Republic of China
| | - Ying Liu
- Department of Oncology, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Baiziting 42, Nanjing, 210009, People's Republic of China
| | - Huanhuan Sha
- Department of Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, 210009, People's Republic of China
| | - Weiwei Peng
- Department of Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, 210009, People's Republic of China
| | - Rong Yin
- Department of Thoracic Surgery, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Jiangsu Cancer Hospital & Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, 210009, People's Republic of China
| | - Guoren Zhou
- Department of Oncology, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Baiziting 42, Nanjing, 210009, People's Republic of China.
| | - Ying Fang
- Department of Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, 210009, People's Republic of China
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8
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Roy A, Sakthikumar S, Kozyrev SV, Nordin J, Pensch R, Mäkeläinen S, Pettersson M, Karlsson EK, Lindblad-Toh K, Forsberg-Nilsson K. Using evolutionary constraint to define novel candidate driver genes in medulloblastoma. Proc Natl Acad Sci U S A 2023; 120:e2300984120. [PMID: 37549291 PMCID: PMC10438395 DOI: 10.1073/pnas.2300984120] [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: 01/17/2023] [Accepted: 07/07/2023] [Indexed: 08/09/2023] Open
Abstract
Current knowledge of cancer genomics remains biased against noncoding mutations. To systematically search for regulatory noncoding mutations, we assessed mutations in conserved positions in the genome under the assumption that these are more likely to be functional than mutations in positions with low conservation. To this end, we use whole-genome sequencing data from the International Cancer Genome Consortium and combined it with evolutionary constraint inferred from 240 mammals, to identify genes enriched in noncoding constraint mutations (NCCMs), mutations likely to be regulatory in nature. We compare medulloblastoma (MB), which is malignant, to pilocytic astrocytoma (PA), a primarily benign tumor, and find highly different NCCM frequencies between the two, in agreement with the fact that malignant cancers tend to have more mutations. In PA, a high NCCM frequency only affects the BRAF locus, which is the most commonly mutated gene in PA. In contrast, in MB, >500 genes have high levels of NCCMs. Intriguingly, several loci with NCCMs in MB are associated with different ages of onset, such as the HOXB cluster in young MB patients. In adult patients, NCCMs occurred in, e.g., the WASF-2/AHDC1/FGR locus. One of these NCCMs led to increased expression of the SRC kinase FGR and augmented responsiveness of MB cells to dasatinib, a SRC kinase inhibitor. Our analysis thus points to different molecular pathways in different patient groups. These newly identified putative candidate driver mutations may aid in patient stratification in MB and could be valuable for future selection of personalized treatment options.
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Affiliation(s)
- Ananya Roy
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 85Uppsala, Sweden
| | - Sharadha Sakthikumar
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 23Uppsala, Sweden
- Broad Institute, Cambridge, MA02142
| | - Sergey V. Kozyrev
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 23Uppsala, Sweden
| | - Jessika Nordin
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 85Uppsala, Sweden
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 23Uppsala, Sweden
| | - Raphaela Pensch
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 23Uppsala, Sweden
| | - Suvi Mäkeläinen
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 23Uppsala, Sweden
| | - Mats Pettersson
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 23Uppsala, Sweden
| | | | - Elinor K. Karlsson
- Broad Institute, Cambridge, MA02142
- Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA01605
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA01605
| | - Kerstin Lindblad-Toh
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 23Uppsala, Sweden
- Broad Institute, Cambridge, MA02142
| | - Karin Forsberg-Nilsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 751 85Uppsala, Sweden
- Division of Cancer and Stem Cells, University of Nottingham Biodiscovery Institute, NottinghamNG72RD, United Kingdom
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9
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Liu T, Zhao M, Peng L, Chen J, Xing P, Gao P, Chen L, Qiao X, Wang Z, Di J, Qu H, Jiang B, Su X. WFDC3 inhibits tumor metastasis by promoting the ERβ-mediated transcriptional repression of TGFBR1 in colorectal cancer. Cell Death Dis 2023; 14:425. [PMID: 37443102 PMCID: PMC10345115 DOI: 10.1038/s41419-023-05956-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 06/20/2023] [Accepted: 07/05/2023] [Indexed: 07/15/2023]
Abstract
Estrogen plays a protective role in colorectal cancer (CRC) and primarily functions through estrogen receptor β (ERβ). However, clinical strategies for CRC therapy associated with ERβ are still under investigation. Our discoveries identified WFDC3 as a tumor suppressor that facilitates estrogen-induced inhibition of metastasis through the ERβ/TGFBR1 signaling axis. WFDC3 interacts with ERβ and increases its protein stability by inhibiting its proteasome-dependent degradation. WFDC3 represses TGFBR1 expression through ERβ-mediated transcription. Blocking TGFβ signaling with galunisertib, a drug used in clinical trials that targets TGFBR1, impaired the migration of CRC cells induced by WFDC3 depletion. Moreover, there was clinical significance to WFDC3 in CRC, as CRC patients with high WFDC3 expression in tumor cells had favorable prognoses. Therefore, this work suggests that WFDC3 could be an indicator for therapies targeting the estrogen/ERβ pathway in CRC patients.
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Affiliation(s)
- Tianqi Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, 100142, Beijing, China
| | - Min Zhao
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore DC, Sunshine Coast, QLD, 4556, Australia
| | - Lin Peng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, 100142, Beijing, China
| | - Jiangbo Chen
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, 100142, Beijing, China
| | - Pu Xing
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, 100142, Beijing, China
| | - Pin Gao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, 100142, Beijing, China
| | - Lei Chen
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, 100142, Beijing, China
| | - Xiaowen Qiao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, 100142, Beijing, China
| | - Zaozao Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, 100142, Beijing, China
| | - Jiabo Di
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, 100142, Beijing, China
| | - Hong Qu
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, 100871, Beijing, People's Republic of China.
| | - Beihai Jiang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, 100142, Beijing, China.
| | - Xiangqian Su
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, 100142, Beijing, China.
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10
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Marin L, Casado F. Prediction of prostate cancer biochemical recurrence by using discretization supports the critical contribution of the extra-cellular matrix genes. Sci Rep 2023; 13:10144. [PMID: 37349324 PMCID: PMC10287745 DOI: 10.1038/s41598-023-35821-1] [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: 01/30/2023] [Accepted: 05/24/2023] [Indexed: 06/24/2023] Open
Abstract
Due to its complexity, much effort has been devoted to the development of biomarkers for prostate cancer that have acquired the utmost clinical relevance for diagnosis and grading. However, all of these advances are limited due to the relatively large percentage of biochemical recurrence (BCR) and the limited strategies for follow up. This work proposes a methodology that uses discretization to predict prostate cancer BCR while optimizing the necessary variables. We used discretization of RNA-seq data to increase the prediction of biochemical recurrence and retrieve a subset of ten genes functionally known to be related to the tissue structure. Equal width and equal frequency data discretization methods were compared to isolate the contribution of the genes and their interval of action, simultaneously. Adding a robust clinical biomarker such as prostate specific antigen (PSA) improved the prediction of BCR. Discretization allowed classifying the cancer patients with an accuracy of 82% on testing datasets, and 75% on a validation dataset when a five-bin discretization by equal width was used. After data pre-processing, feature selection and classification, our predictions had a precision of 71% (testing dataset: MSKCC and GSE54460) and 69% (Validation dataset: GSE70769) should the patients present BCR up to 24 months after their final treatment. These results emphasize the use of equal width discretization as a pre-processing step to improve classification for a limited number of genes in the signature. Functionally, many of these genes have a direct or expected role in tissue structure and extracellular matrix organization. The processing steps presented in this study are also applicable to other cancer types to increase the speed and accuracy of the models in diverse datasets.
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Affiliation(s)
- Laura Marin
- Department of Engineering, Pontificia Universidad Catolica del Peru, Av. Universitaria 1801, San Miguel, 15088, Lima, Peru
- Institute of Omics Sciences and Applied Biotechnology, Pontificia Universidad Catolica del Peru, Av. Universitaria 1801, San Miguel, 15088, Lima, Peru
| | - Fanny Casado
- Institute of Omics Sciences and Applied Biotechnology, Pontificia Universidad Catolica del Peru, Av. Universitaria 1801, San Miguel, 15088, Lima, Peru.
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11
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Braun F, Jaschinski M, Täger P, Marmann V, Brandenstein MV, Köditz B, Fischer T, Muñoz-Vázquez S, Zimmermanns B, Dietlein M, Sudbrock F, Krapf P, Fischer D, Heidenreich A, Drzezga A, Kirsch S, Pietsch M, Schomäcker K. Synthesis and evaluation of radioiodinated estrogens for diagnosis and therapy of male urogenital tumours. Org Biomol Chem 2023; 21:3090-3095. [PMID: 36947011 DOI: 10.1039/d3ob00114h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
The preparation of 24 estrogens, their estrogen receptor (ER) affinity and studies of radioiodinated estrogen binding to ER-positive male bladder tumor cells (HTB9) are described. The estrogens with the highest affinity were selected using fluorescence anisotropy assays. A 2,2,2-trifluoroethyl group at the 11β-position caused particularly promising affinity. (Radio)iodination was performed on the 17α-vinyl group. Binding studies on HTB9 cells revealed picomolar affinities of radioconjugates 19 and 31, indicating promising ability for targeting of urogenital tumors.
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Affiliation(s)
- Feodor Braun
- Department of Nuclear Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937, Cologne, Germany.
| | - Marcel Jaschinski
- Organic Chemistry, Bergische Universität Wuppertal, 42119 Wuppertal, Germany
| | - Philipp Täger
- Department of Nuclear Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937, Cologne, Germany.
| | - Verena Marmann
- Department of Nuclear Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937, Cologne, Germany.
| | - Melanie von Brandenstein
- Clinic and Polyclinic for Urology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Barbara Köditz
- Clinic and Polyclinic for Urology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Thomas Fischer
- Department of Nuclear Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937, Cologne, Germany.
| | - Sergio Muñoz-Vázquez
- Department of Nuclear Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937, Cologne, Germany.
| | - Beate Zimmermanns
- Department of Nuclear Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937, Cologne, Germany.
| | - Markus Dietlein
- Department of Nuclear Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937, Cologne, Germany.
| | - Ferdinand Sudbrock
- Department of Nuclear Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937, Cologne, Germany.
| | - Phillip Krapf
- Department of Nuclear Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937, Cologne, Germany.
| | - Dietmar Fischer
- Institutes I & II of Pharmacology, Center of Pharmacology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Axel Heidenreich
- Clinic and Polyclinic for Urology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Alexander Drzezga
- Department of Nuclear Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937, Cologne, Germany.
| | - Stefan Kirsch
- Organic Chemistry, Bergische Universität Wuppertal, 42119 Wuppertal, Germany
| | - Markus Pietsch
- Institutes I & II of Pharmacology, Center of Pharmacology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Klaus Schomäcker
- Department of Nuclear Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937, Cologne, Germany.
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12
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Stevens C, Hightower A, Buxbaum SG, Falzarano SM, Rhie SK. Genomic, epigenomic, and transcriptomic signatures of prostate cancer between African American and European American patients. Front Oncol 2023; 13:1079037. [PMID: 36937425 PMCID: PMC10018228 DOI: 10.3389/fonc.2023.1079037] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 02/10/2023] [Indexed: 03/06/2023] Open
Abstract
Prostate cancer is the second most common cancer in men in the United States, and racial disparities are greatly observed in the disease. Specifically, African American (AA) patients have 60% higher incidence and mortality rates, in addition to higher grade and stage prostate tumors, than European American (EA) patients. In order to narrow the gap between clinical outcomes for these two populations, genetic and molecular signatures contributing to this disparity have been characterized. Over the past decade, profiles of prostate tumor samples from different ethnic groups have been developed using molecular and functional assays coupled with next generation sequencing or microarrays. Comparative genome-wide analyses of genomic, epigenomic, and transcriptomic profiles from prostate tumor samples have uncovered potential race-specific mutations, copy number alterations, DNA methylation, and gene expression patterns. In this study, we reviewed over 20 published studies that examined the aforementioned molecular contributions to racial disparities in AA and EA prostate cancer patients. The reviewed genomic studies revealed mutations, deletions, amplifications, duplications, or fusion genes differentially enriched in AA patients relative to EA patients. Commonly reported genomic alterations included mutations or copy number alterations of FOXA1, KMT2D, SPOP, MYC, PTEN, TP53, ZFHX3, and the TMPRSS2-ERG fusion. The reviewed epigenomic studies identified that CpG sites near the promoters of PMEPA1, RARB, SNRPN, and TIMP3 genes were differentially methylated between AA and EA patients. Lastly, the reviewed transcriptomic studies identified genes (e.g. CCL4, CHRM3, CRYBB2, CXCR4, GALR1, GSTM3, SPINK1) and signaling pathways dysregulated between AA and EA patients. The most frequently found dysregulated pathways were involved in immune and inflammatory responses and neuroactive ligand signaling. Overall, we observed that the genomic, epigenomic, and transcriptomic alterations evaluated between AA and EA prostate cancer patients varied between studies, highlighting the impact of using different methods and sample sizes. The reported genomic, epigenomic, and transcriptomic alterations do not only uncover molecular mechanisms of tumorigenesis but also provide researchers and clinicians valuable resources to identify novel biomarkers and treatment modalities to improve the disparity of clinical outcomes between AA and EA patients.
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Affiliation(s)
- Claire Stevens
- Department of Biochemistry and Molecular Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine of USC, Los Angeles, CA, United States
- CaRE2 Program, Florida-California Health Equity Center, Los Angeles, CA, United States
| | - Alexandria Hightower
- Department of Biochemistry and Molecular Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine of USC, Los Angeles, CA, United States
- CaRE2 Program, Florida-California Health Equity Center, Los Angeles, CA, United States
| | - Sarah G. Buxbaum
- CaRE2 Program, Florida-California Health Equity Center, Los Angeles, CA, United States
- Department of Epidemiology and Biostatistics, College of Pharmacy and Pharmaceutical Sciences, Institute of Public Health, Florida A&M University, Tallahassee, FL, United States
| | - Sara M. Falzarano
- CaRE2 Program, Florida-California Health Equity Center, Los Angeles, CA, United States
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, FL, United States
| | - Suhn K. Rhie
- Department of Biochemistry and Molecular Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine of USC, Los Angeles, CA, United States
- CaRE2 Program, Florida-California Health Equity Center, Los Angeles, CA, United States
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13
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Li M, Zheng Y, Li X, Shen X, Zhang T, Weng B, Mao H, Zhao J. ATBF1 is a potential diagnostic marker of histological grade and functions via WNT5A in breast cancer. BMC Cancer 2022; 22:1280. [PMID: 36476423 PMCID: PMC9727999 DOI: 10.1186/s12885-022-10380-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Histological grade has been demonstrated to be an important factor of breast cancer outcome and is associated with cell differentiation and is currently being evaluated via H&E-stained sections. Molecular biomarkers are essential to improve the accuracy of histological grading. ATBF1, a large transcription factor, has been considered a tumor suppressor gene with frequent mutations or deletions in multiple cancers. In breast cancer, ATBF1 was reported to function in cell differentiation and mammary development. However, its role in the clinic has rarely been reported. METHODS Breast cancer tissues (BCTs) and adjacent noncancerous tissues (ANCTs) were collected to analyze the expression of ATBF1 at the mRNA and protein levels. Three anti-ATBF1 antibodies recognizing independent peptides of ATBF1 (N-terminal end, middle region and C-terminal end) were applied for IHC staining. Small interfering RNA (siRNA) was used to silence ATBF1 expression and to investigate the roles of ATBF1 in MCF7 cells. Microarrays were introduced to analyze the differentially expressed genes, enriched GO terms and KEGG terms regulated by ATBF1 and its potential downstream genes, which were further confirmed in vitro and in clinical samples. RESULTS The expression of ATBF1 was reduced in BCTs at both the mRNA and protein levels compared with that in ANCTs. ATBF1 protein was predominantly localized in the nucleus of ANCTs but in the cytoplasm of BCTs. Both the mRNA and protein levels of ATBF1 were significantly correlated with histological grade. Consistently, knockdown of ATBF1 increased stemness marker expression and reduced differentiation markers in vitro. Further analysis identified WNT5A as an essential downstream gene of ATBF1 in breast cancer cells. Treatment of WNT5A disrupted cell proliferation induced by ATBF1 silencing. In BCTs, a significant correlation was observed between the expression of WNT5A and ATBF1. CONCLUSION The results indicated that ATBF1 expression might be a useful diagnostic marker associated with histological grade and breast cancer malignancy. WNT5A and its signaling pathway are novel mechanisms by which ATBF1 contributes to breast cancer tumorigenesis.
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Affiliation(s)
- Mei Li
- grid.203507.30000 0000 8950 5267Zhejiang Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, 818 Fenghua Road, Ningbo, Zhejiang 315211 China ,Ningbo Institute of Medical Sciences, Ningbo, Zhejiang China
| | - Yanan Zheng
- grid.203507.30000 0000 8950 5267Zhejiang Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, 818 Fenghua Road, Ningbo, Zhejiang 315211 China
| | - Xujun Li
- grid.9227.e0000000119573309Department of Breast Surgery, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, Zhejiang China
| | - Xiaohan Shen
- Ningbo Diagnostic Pathology Center, Ningbo, Zhejiang China
| | - Tingxia Zhang
- grid.203507.30000 0000 8950 5267Zhejiang Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, 818 Fenghua Road, Ningbo, Zhejiang 315211 China
| | - Bowen Weng
- grid.203507.30000 0000 8950 5267Zhejiang Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, 818 Fenghua Road, Ningbo, Zhejiang 315211 China
| | - Haijiao Mao
- grid.203507.30000 0000 8950 5267Department of Orthopaedic Surgery, the Affiliated Hospital of Medical School, Ningbo University, Ningbo, Zhejiang China
| | - Jiyuan Zhao
- grid.203507.30000 0000 8950 5267Zhejiang Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, 818 Fenghua Road, Ningbo, Zhejiang 315211 China
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14
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Liu Z, Elcheva I. A six-gene prognostic signature for both adult and pediatric acute myeloid leukemia identified with machine learning. Am J Transl Res 2022; 14:6210-6221. [PMID: 36247279 PMCID: PMC9556437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 07/19/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Although it is well-known that adult and pediatric acute myeloid leukemias (AMLs) are genetically distinct diseases, they still share certain gene expression profiles. The age-related genetic heterogeneities of AMLs have been well-studied, but the common prognostic signatures and molecular mechanisms of adult and pediatric AMLs are less investigated. AIM To identify genes and pathways that are associated with both pediatric and adult AMLs and discover a gene signature for overall survival (OS) prediction. METHODS Through mining the transcriptome profiles of The Cancer Genome Atlas (TCGA) data sets of adult cancers and The Therapeutically Applicable Research to Generate Effective Treatments (TARGET) data of pediatric cancers, we identified genes that are commonly dysregulated in both pediatric and adult AMLs, further discovered a common gene signature, and built two risk score models for TCGA and TARGET cohorts, respectively with L 0 regularized global AUC (area under the receiver operating characteristic curve) summary maximization. RESULTS We identified 57 genes that are differentially expressed and prognostically significant in both adult and childhood AMLs. The top 4 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enriched with those 57 genes include transcriptional misregulation, focal adhesion, PI3K-Akt signaling pathway, and signaling pathways regulating pluripotency of stem cells. We further identified a 6-gene signature including genes of ADAMTS3, DNMT3B, NYNRIN, SORT1, ZFHX3, and ZG16B for risk prediction. We constructed a risk score model with one dataset (either TCGA or TARGET) and evaluated its performance with the other. The test AUCs for the risk prediction of TCGA data with a 2-year and 5-year OS cutoffs are 0.762 (P = 2.33e-13, 95% CI: 0.69-0.83) and 0.759 (P = 7.26e-08, 95% CI: 0.66-0.85), respectively, while the test AUCs of TARGET data with the same cutoffs are 0.71 (P = 3.3e-07, 95% CI: 0.62-0.79) and 0.72 (P= 5.25e-09, 95% CI: 0.65-0.80), respectively. We further stratified patients into 3 equal sized prognostic subtypes with the 6-gene risk scores. The P-values of the tertile partitions are 1.74e-07 and 3.28e-08 for the TARGET and TCGA cohorts, respectively, which are significantly better than the standard cytogenetic risk stratification of both cohorts (TARGET: P = 1.64e-06; TCGA: P = 1.79e-05). When validated with two other independent cohorts, the 6-gene risk score models remain a significant predictor for OS. Investigating the common gene expression program is significant in that we may extrapolate the findings from adults to children and avoid unnecessary pediatric clinical trials.
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Affiliation(s)
- Zhenqiu Liu
- Department of Public Health Sciences, Pennsylvania State University College of Medicine500 University Drive, Hershey, PA 17033, USA
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Penn State College of Medicine500 University Drive, Hershey, PA 17033, USA
| | - Irina Elcheva
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Penn State College of Medicine500 University Drive, Hershey, PA 17033, USA
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15
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Liu J, Tan Z, Yang S, Song X, Li W. A circadian rhythm-related gene signature for predicting relapse risk and immunotherapeutic effect in prostate adenocarcinoma. Aging (Albany NY) 2022; 14:7170-7185. [PMID: 36103249 PMCID: PMC9512510 DOI: 10.18632/aging.204288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 09/05/2022] [Indexed: 11/25/2022]
Affiliation(s)
- Jin Liu
- Department of Urology, The Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Zhao Tan
- Department of Urology, The Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Shijie Yang
- Department of Urology, The Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Xinda Song
- Department of Urology, The Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Wenping Li
- Department of Urology, The Third Hospital of Hebei Medical University, Shijiazhuang, China
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16
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Lee S, Osmanbeyoglu HU. Chromatin accessibility landscape and active transcription factors in primary human invasive lobular and ductal breast carcinomas. BREAST CANCER RESEARCH : BCR 2022; 24:54. [PMID: 35906698 PMCID: PMC9338552 DOI: 10.1186/s13058-022-01550-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 07/25/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND Invasive lobular breast carcinoma (ILC), the second most prevalent histological subtype of breast cancer, exhibits unique molecular features compared with the more common invasive ductal carcinoma (IDC). While genomic and transcriptomic features of ILC and IDC have been characterized, genome-wide chromatin accessibility pattern differences between ILC and IDC remain largely unexplored. METHODS Here, we characterized tumor-intrinsic chromatin accessibility differences between ILC and IDC using primary tumors from The Cancer Genome Atlas (TCGA) breast cancer assay for transposase-accessible chromatin with sequencing (ATAC-seq) dataset. RESULTS We identified distinct patterns of genome-wide chromatin accessibility in ILC and IDC. Inferred patient-specific transcription factor (TF) motif activities revealed regulatory differences between and within ILC and IDC tumors. EGR1, RUNX3, TP63, STAT6, SOX family, and TEAD family TFs were higher in ILC, while ATF4, PBX3, SPDEF, PITX family, and FOX family TFs were higher in IDC. CONCLUSIONS This study reveals the distinct epigenomic features of ILC and IDC and the active TFs driving cancer progression that may provide valuable information on patient prognosis.
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Affiliation(s)
- Sanghoon Lee
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, USA.,UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, USA
| | - Hatice Ulku Osmanbeyoglu
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, USA. .,Department of Bioengineering, School of Engineering, University of Pittsburgh, Pittsburgh, USA. .,UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, USA. .,Department of Biostatistics, School of Public Health, University of Pittsburgh, Pittsburgh, USA.
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17
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Wang Y, Huang B, Fu Q, Wang J, Ye M, Hu M, Qu K, Liu K, Hu X, Wei S, Sun K, Xiao W, Zhang B, Li H, Li J, Zhang Q, Liang T. Comprehensive Clinical Analysis of Gallbladder Neuroendocrine Neoplasms: A Large-Volume Multicenter Study During One Decade. Ann Surg Oncol 2022; 29:7619-7630. [PMID: 35849293 DOI: 10.1245/s10434-022-12107-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 06/05/2022] [Indexed: 02/06/2023]
Abstract
BACKGROUND This study aimed to comprehensively investigate the clinicopathologic characteristics and therapeutic situations of gallbladder neuroendocrine neoplasms (GB-NENs) in the real world via a multicenter, large-scale cohort study. METHODS The study searched for patients in 143 hospitals in China and enrolled 154 patients with GB-NENs diagnosed in 40 hospitals between 2004 and 2021. Clinicopathologic characteristics and therapeutic approaches were analyzed retrospectively. RESULTS The median age at the initial diagnosis of the patients with GB-NENs was 63 years (range 33-83 years), and 61.7% of the patients were women. Tumor-node-metastasis staging classified 92 patients as stage 3 or above. Based on the 2019 World Health Organization classification, 96 cases (62.3%) were confirmed pathologically as poorly differentiated neuroendocrine carcinomas, 13 cases (8.4%) as well-differentiated neuroendocrine tumors, and 45 cases as mixed neuroendocrine-non-neuroendocrine neoplasms. The liver was the most frequent metastatic site. Immunohistochemistry showed that synaptophysin was most frequently positive (80.4%), followed by chromogranin A (61.7%), and CD56 (58.4%). Computed tomography and magnetic resonance imaging showed more common clear boundaries (25/39 cases) and invasive growth features (27 cases). None of these cases had an accurate diagnosis before surgery, with a misdiagnosis rate of 100%. Surgical resection is the main treatment, and platinum-based chemotherapeutic regimens were preferred as adjuvant therapies for patients with GB-NENs. The available survival data for 74 patients showed an overall survival rate of 59% at 1 year, 33% at 3 years, and 29% at 5 years. No significant difference was found between the patients treated with and those treated without adjuvant chemotherapy. CONCLUSIONS Gallbladder neuroendocrine neoplasms have high malignancy and a poor prognosis. Importantly, this large-scale cohort study significantly improves our understanding of GB-NENs and will benefit the exploration of its mechanism and treatment modes. Further investigation is necessary to explore the management of this disease.
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Affiliation(s)
- Yangyang Wang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Bingfeng Huang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qihan Fu
- Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, China.,Zhejiang University Cancer Center, Hangzhou, China.,Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jianing Wang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Mao Ye
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Manyi Hu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Kai Qu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Kai Liu
- Department of Hepatobiliary and Pancreatic Surgery, The First Hospital of Jilin University, Changchun, China
| | - Xiao Hu
- Department of Hepatobiliary Pancreatic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Shumei Wei
- Department of Pathology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ke Sun
- Department of Pathology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wenbo Xiao
- Department of Radiology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Bo Zhang
- Department of General Surgery, Shenzhen University Luohu People's Hospital, Shenzhen, China
| | - Haijun Li
- Department of General Surgery, Shenzhen University Luohu People's Hospital, Shenzhen, China
| | - Jingsong Li
- The Engineering Research Center of EMR and Intelligent Expert System, Ministry of Education, College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, China.,Research Center for Healthcare Data Science, Zhejiang Lab, Hangzhou, China
| | - Qi Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China. .,Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China. .,Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, China. .,Zhejiang University Cancer Center, Hangzhou, China.
| | - Tingbo Liang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China. .,Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China. .,Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, China. .,Zhejiang University Cancer Center, Hangzhou, China.
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18
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Weitz P, Wang Y, Kartasalo K, Egevad L, Lindberg J, Grönberg H, Eklund M, Rantalainen M. Transcriptome-wide prediction of prostate cancer gene expression from histopathology images using co-expression based convolutional neural networks. Bioinformatics 2022; 38:3462-3469. [PMID: 35595235 PMCID: PMC9237721 DOI: 10.1093/bioinformatics/btac343] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 03/18/2022] [Accepted: 05/16/2022] [Indexed: 12/15/2022] Open
Abstract
Motivation Molecular phenotyping by gene expression profiling is central in contemporary cancer research and in molecular diagnostics but remains resource intense to implement. Changes in gene expression occurring in tumours cause morphological changes in tissue, which can be observed on the microscopic level. The relationship between morphological patterns and some of the molecular phenotypes can be exploited to predict molecular phenotypes from routine haematoxylin and eosin-stained whole slide images (WSIs) using convolutional neural networks (CNNs). In this study, we propose a new, computationally efficient approach to model relationships between morphology and gene expression. Results We conducted the first transcriptome-wide analysis in prostate cancer, using CNNs to predict bulk RNA-sequencing estimates from WSIs for 370 patients from the TCGA PRAD study. Out of 15 586 protein coding transcripts, 6618 had predicted expression significantly associated with RNA-seq estimates (FDR-adjusted P-value <1×10−4) in a cross-validation and 5419 (81.9%) of these associations were subsequently validated in a held-out test set. We furthermore predicted the prognostic cell-cycle progression score directly from WSIs. These findings suggest that contemporary computer vision models offer an inexpensive and scalable solution for prediction of gene expression phenotypes directly from WSIs, providing opportunity for cost-effective large-scale research studies and molecular diagnostics. Availability and implementation A self-contained example is available from http://github.com/phiwei/prostate_coexpression. Model predictions and metrics are available from doi.org/10.5281/zenodo.4739097. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Philippe Weitz
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, 17177, Sweden
| | - Yinxi Wang
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, 17177, Sweden
| | - Kimmo Kartasalo
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, 17177, Sweden.,Faculty of Medicine and Health Technology, Tampere University, Tampere, 33100, Finland
| | - Lars Egevad
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, 17177, Sweden
| | - Johan Lindberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, 17177, Sweden.,Science for Life Laboratory, Stockholm, 17177, Sweden
| | - Henrik Grönberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, 17177, Sweden
| | - Martin Eklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, 17177, Sweden
| | - Mattias Rantalainen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, 17177, Sweden
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19
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Zhang Y, Chen F, Chandrashekar DS, Varambally S, Creighton CJ. Proteogenomic characterization of 2002 human cancers reveals pan-cancer molecular subtypes and associated pathways. Nat Commun 2022; 13:2669. [PMID: 35562349 PMCID: PMC9106650 DOI: 10.1038/s41467-022-30342-3] [Citation(s) in RCA: 78] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 04/25/2022] [Indexed: 12/12/2022] Open
Abstract
Mass-spectrometry-based proteomic data on human tumors—combined with corresponding multi-omics data—present opportunities for systematic and pan-cancer proteogenomic analyses. Here, we assemble a compendium dataset of proteomics data of 2002 primary tumors from 14 cancer types and 17 studies. Protein expression of genes broadly correlates with corresponding mRNA levels or copy number alterations (CNAs) across tumors, but with notable exceptions. Based on unsupervised clustering, tumors separate into 11 distinct proteome-based subtypes spanning multiple tissue-based cancer types. Two subtypes are enriched for brain tumors, one subtype associating with MYC, Wnt, and Hippo pathways and high CNA burden, and another subtype associating with metabolic pathways and low CNA burden. Somatic alteration of genes in a pathway associates with higher pathway activity as inferred by proteome or transcriptome data. A substantial fraction of cancers shows high MYC pathway activity without MYC copy gain but with mutations in genes with noncanonical roles in MYC. Our proteogenomics survey reveals the interplay between genome and proteome across tumor lineages. Pan-cancer proteomics analysis enables the analysis of protein expression across multiple cancer types. Here, the authors compare proteomics from 14 cancer types and show 11 distinct subtypes across multiple cancer types. Proteome data could link higher pathway activity levels with somatic alteration of specific genes in the pathway.
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Affiliation(s)
- Yiqun Zhang
- Dan L. Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX, USA
| | - Fengju Chen
- Dan L. Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX, USA
| | - Darshan S Chandrashekar
- Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, 35233, USA.,Division of Molecular and Cellular Pathology, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Sooryanarayana Varambally
- Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, 35233, USA.,Division of Molecular and Cellular Pathology, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, 35233, USA.,The Informatics Institute, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Chad J Creighton
- Dan L. Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX, USA. .,Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. .,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
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20
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Clinical utility of PDX cohorts to reveal biomarkers of intrinsic resistance and clonal architecture changes underlying acquired resistance to cetuximab in HNSCC. Signal Transduct Target Ther 2022; 7:73. [PMID: 35260570 PMCID: PMC8904860 DOI: 10.1038/s41392-022-00908-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 02/07/2023] Open
Abstract
Cetuximab is a widely used drug for treating head and neck squamous cell carcinomas (HNSCCs); however, it provides restricted clinical benefits, and its response duration is limited by drug resistance. Here, we conducted randomized “Phase II-like clinical trials” of 49 HNSCC PDX models and reveal multiple informative biomarkers for intrinsic resistance to cetuximab (e.g., amplification of ANKH, up-regulation of PARP3). After validating these intrinsic resistance biomarkers in another HNSCC PDX cohort (61 PDX models), we generated acquired cetuximab resistance PDX models and analyzed them to uncover resistance mechanisms. Whole exome sequencing and transcriptome sequencing revealed diverse patterns of clonal selection in acquired resistant PDXs, including the emergence of subclones with strongly activated RAS/MAPK. Extending these insights, we show that a combination of a RAC1/RAC3 dual-target inhibitor and cetuximab could overcome acquired cetuximab resistance in vitro and in vivo. Beyond revealing intrinsic resistance biomarkers, our PDX-based study shows how clonal architecture changes underlying acquired resistance can be targeted to expand the therapeutic utility of this important drug to more HNSCC patients.
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21
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Chen J, Liu W, Du J, Wang P, Wang J, Ye K. Comprehensive Genomic and Epigenomic Analyses on Transcriptomic Regulation in Stomach Adenocarcinoma. Front Genet 2022; 12:778095. [PMID: 35222516 PMCID: PMC8873582 DOI: 10.3389/fgene.2021.778095] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 12/28/2021] [Indexed: 12/24/2022] Open
Abstract
Background: DNA methylation (MET)–mediated transcriptomic disturbance and copy number variations (CNVs) exert a significant influence in stimulating the heterogeneous progression of stomach adenocarcinoma (STAD). Nevertheless, the relation of DNA MET with CNVs, together with its impact on tumor occurrence, is still unclear.Methods: The messenger RNA (mRNA) expression (EXP) profiles, DNA MET, and DNA copy numbers, together with STAD mutation data, were collected from the TCGA official data portal. We employed circular binary segmentation algorithm in “DNAcopy.” library of R package for mapping DNA CNV data at genetic level for all samples based on the segmented CNV data. Stable clusters of samples were recognized using negative matrix factorization cluster analysis based on 50 iterations and the “brunet” method using the MET-correlated (METcor) and CNV-correlated (CNVcor) genes. The R package “iCluster” method was utilized to comprehensively analyze the EXP, MET, and DNA CNV profiles.Results: A total of 313 STAD samples were isolated for checking DNA copy numbers and MET and for measuring EXP. In accordance with our results, we discovered obvious co-regulation of CNVcor genes and METcor counterparts. Apart from that, these genes were subject to multi-omics integration. Meanwhile, three subtypes of STAD were detected and confirmed based on independent data. Among them, the subtype with increased aggressiveness was related to decreased mutation frequencies of ARID1A, PIK3CA, ZFHX3, SPECC1, OBSCN, KMT2D, FSIP2, ZBTB20, TTN, and RANBP2, together with the abnormal levels of JPH3, KCNB1, and PLCXD3.Conclusion: According to the results, these aforementioned genes exerted crucial roles in the development of invasive STAD. Our findings on transcriptomic regulation genomically and epigenetically facilitate the understanding of the STAD pathology from different aspects, which help to develop efficient anti-STAD therapy.
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22
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Jiang Y, Chan CKW, Chan RCK, Wang X, Wong N, To KF, Ng SSM, Lau JYW, Poon CCY. Identification of Tissue Types and Gene Mutations From Histopathology Images for Advancing Colorectal Cancer Biology. IEEE OPEN JOURNAL OF ENGINEERING IN MEDICINE AND BIOLOGY 2022; 3:115-123. [PMID: 35937101 PMCID: PMC9355144 DOI: 10.1109/ojemb.2022.3192103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/12/2022] [Accepted: 06/22/2022] [Indexed: 12/24/2022] Open
Abstract
Objective: Colorectal cancer (CRC) patients respond differently to treatments and are sub-classified by different approaches. We evaluated a deep learning model, which adopted endoscopic knowledge learnt from AI-doscopist, to characterise CRC patients by histopathological features. Results: Data of 461 patients were collected from TCGA-COAD database. The proposed framework was able to 1) differentiate tumour from normal tissues with an Area Under Receiver Operating Characteristic curve (AUROC) of 0.97; 2) identify certain gene mutations (MYH9, TP53) with an AUROC > 0.75; 3) classify CMS2 and CMS4 better than the other subtypes; and 4) demonstrate the generalizability of predicting KRAS mutants in an external cohort. Conclusions: Artificial intelligent can be used for on-site patient classification. Although KRAS mutants were commonly associated with therapeutic resistance and poor prognosis, subjects with predicted KRAS mutants in this study have a higher survival rate in 30 months after diagnoses.
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Affiliation(s)
- Yuqi Jiang
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong SAR
| | - Cecilia K. W. Chan
- Division of Vascular and General Surgery, Department of Surgery, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR
| | - Ronald C. K. Chan
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong SAR
| | - Xin Wang
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong SAR
| | - Nathalie Wong
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong SAR
| | - Ka Fai To
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong SAR
| | - Simon S. M. Ng
- Division of Colorectal Surgery, Department of Surgery, The Chinese University of Hong Kong, Hong Kong SAR
| | - James Y. W. Lau
- Division of Vascular and General Surgery, Department of Surgery, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR
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23
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Kakoo A, Al-Attar M, Rasheed T. Exonic variants in multiple myeloma patients associated with relapsed/ refractory and response to bortezomib regimens. Saudi J Biol Sci 2022; 29:610-614. [PMID: 35002457 PMCID: PMC8716956 DOI: 10.1016/j.sjbs.2021.09.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 09/08/2021] [Accepted: 09/09/2021] [Indexed: 11/30/2022] Open
Abstract
Novel treatment in multiple myeloma represented by proteasome inhibitors, immunomodulatory drugs and monoclonal antibodies have produced a deep response. However, relapses are possible, and all classes of drugs are refractory to patients. Next-generation sequencing has improved our understanding of the multiple myeloma genome related to drug resistance and has discovered many genomic variants. Therefore, this study was conducted to investigate new variants associated with drug resistance in MM patients who relapsed and refractory to bortezomib regimen and daratumumab treatment using next-generation sequencing for whole-exome sequencing. Peripheral blood samples were collected in EDTA tubes from six patients; four were in relapsed and refractory to bortezomib regimens and daratumumab; two patients responded to bortezomib regimens. Whole-exome sequencing was performed by the MGI-DNBSEQ-G400 instrument. We identified 21 variants in multiple myeloma patients. Seventeen variants were found in relapsed and refractory multiple myeloma in 11 genes (GNAQ, PMS1, CREB1, NSUNS2, PIK3CG, ROS1, PMS2, FIT4, KDM5A, STK11 and ZFHX3). And four variants were identified in two patients with response to bortezomib regimens in 4 genes (RAF1, CREB1, ZFHX3 and INSR). We have observed several genetic variants in many genes that may have been associated with the poor prognosis and poor response to treatment in these patients. These values should be further confirmed in large sample studies using the RNA-seq technique to identify genome expression.
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Key Words
- BCL-2, B-cell lymphoma 2
- BWA, Burrows-Wheeler Aligner
- GATK, Genome Analysis Toolkit
- IGV, Integrative Genomic Viewer
- MAPK, mitogen-activated protein
- MCL-1, myeloid cell leukaemia-1
- MM, multiple myeloma
- MMR, mismatch repair
- Multiple myeloma
- M−CSF, macrophage colony-stimulating factor
- NF-кB, nuclear factor kappa B
- NGS, Next-generation sequence
- Next-generation sequencing
- RANKL, receptor activator of nuclear factors-кB ligand
- RTKs, tyrosine kinases receptors
- SNP, single nucleotide polymorphism
- VEGF-C, vascular endothelial growth factors receptors
- VUS, variant unknown significant
- WES, whole exome sequence
- drug resistance
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Affiliation(s)
- Ashraf Kakoo
- Department- College of Science, Salahaddin University, Erbil, Iraq
| | - Mustafa Al-Attar
- Department- College of Science, Salahaddin University, Erbil, Iraq
| | - Taban Rasheed
- Department- College of Science, Salahaddin University, Erbil, Iraq
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24
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Fu X, Zhang Z, Liu M, Li J, A J, Fu L, Huang C, Dong JT. AR imposes different effects on ZFHX3 transcription depending on androgen status in prostate cancer cells. J Cell Mol Med 2021; 26:800-812. [PMID: 34953044 PMCID: PMC8817138 DOI: 10.1111/jcmm.17125] [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: 09/09/2021] [Revised: 11/11/2021] [Accepted: 11/29/2021] [Indexed: 12/24/2022] Open
Abstract
Both androgen receptor (AR) and the ZFHX3 transcription factor modulate prostate development. While AR drives prostatic carcinogenesis, ZFHX3 is a tumour suppressor whose loss activates the PI3K/AKT signalling in advanced prostate cancer (PCa). However, it is unknown whether ZFHX3 and AR are functionally related in PCa cells and, if so, how. Here, we report that in AR-positive LNCaP and C4-2B PCa cells, androgen upregulates ZFHX3 transcription via androgen-induced AR binding to the androgen-responsive elements (AREs) of the ZFHX3 promoter. Androgen also upregulated ZFHX3 transcription in vivo, as castration dramatically reduced Zfhx3 mRNA and protein levels in mouse prostates, and ZFHX3 mRNA levels correlated with AR activities in human PCa. Interestingly, the binding of AR to one ARE occurred in the absence of androgen, and the binding repressed ZFHX3 transcription as this repressive binding was interrupted by androgen treatment. The enzalutamide antiandrogen prevented androgen from inducing ZFHX3 transcription and caused excess ZFHX3 protein degradation. In human PCa, ZFHX3 was downregulated and the downregulation correlated with worse patient survival. These findings establish a regulatory relationship between AR and ZFHX3, suggest a role of ZFHX3 in AR function and implicate ZFHX3 loss in the antiandrogen therapies of PCa.
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Affiliation(s)
- Xing Fu
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, China.,Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Zhiqian Zhang
- Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Mingcheng Liu
- Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Juan Li
- Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Jun A
- Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Liya Fu
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Chenyang Huang
- Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Jin-Tang Dong
- Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, Shenzhen, China
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25
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Zhang L, Wang Y, Li Z, Lin D, Liu Y, Zhou L, Wang D, Wu A, Li Z. Clinicopathological features of tumor mutation burden, Epstein-Barr virus infection, microsatellite instability and PD-L1 status in Chinese patients with gastric cancer. Diagn Pathol 2021; 16:38. [PMID: 33933102 PMCID: PMC8088709 DOI: 10.1186/s13000-021-01099-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 04/15/2021] [Indexed: 01/10/2023] Open
Abstract
Objectives Gastric cancer (GC) is the 4th most common type of cancer worldwide. Different GC subtypes have unique molecular features that may have different therapeutic methods. The aim of the present study was to investigate Epstein-Barr virus (EBV) infection, microsatellite instability (MSI) status, the expression of programmed death-ligand 1 (PD-L1) and gene mutations in GC patients. Methods The data of 2504 GC patients, who underwent curative gastrectomy with lymphadenectomy at Peking University Cancer Hospital between 2013 and 2018, were reviewed. We analyzed the clinicopathological factors associated with the immunohistochemistry (IHC) profiles of these patients, and genetic alterations were analyzed using next generation sequencing (NGS). Results Mismatch repair-deficient (d-MMR) GC patients were found to have a higher probability of expressing PD-L1 (p = 0.000, PD-L1 cutoff value = 1%). In addition, 4 and 6.9% of the 2504 gastric cancer patients were EBV-positive and d-MMR, respectively. The number of MLH1/PMS2-negative cases was 126 (6%), and the number of MSH2/MSH6-negative cases was 14 (0.9%). d-MMR status was associated with a intestinal group (p = 0.012), but not with tumor differentiation. Furthermore, MSI and d-MMR GC status (detected by NGS and IHC, respectively) were consistently high, and the rate of MSI was higher in patients with d-MMR GC. A number of genes associated with DNA damage repair were detected in GC patients with MSI, including POLE, ETV6, BRCA and RNF43. In patients with a high tumor mutation burden, the most significantly mutated genes were LRP1B (79.07%), ARID1A (74.42%), RNF43 (69.77%), ZFHX3 (65.12%), TP53 (58.14%), GANS (51.16%), BRCA2 (51.16%), PIK3CA (51.16%), NOTCH1 (51.16%), SMARCA4 (48.84%), ATR (46.51%), POLE (41.86%) and ATM (39.53%). Conclusions Using IHC and NGS, MSI status, protein expression, tumor mutation burden (TMB) and genetic alterations were identified in patients with GC, which provides a theoretical basis for the future clinical treatment of GC.
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Affiliation(s)
- Li Zhang
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research, Peking University Cancer Hospital, No.52 Fucheng Road Haidian District, Beijing, 100142, People's Republic of China
| | - Yinkui Wang
- Department of Gastrointestinal Surgery, Key Laboratory of Carcinogenesis and Translational Research, Peking University Cancer Hospital, No.52 Fucheng Road Haidian District, Beijing, 100142, People's Republic of China
| | - Zhongwu Li
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research, Peking University Cancer Hospital, No.52 Fucheng Road Haidian District, Beijing, 100142, People's Republic of China
| | - Dongmei Lin
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research, Peking University Cancer Hospital, No.52 Fucheng Road Haidian District, Beijing, 100142, People's Republic of China
| | - Yiqiang Liu
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research, Peking University Cancer Hospital, No.52 Fucheng Road Haidian District, Beijing, 100142, People's Republic of China.,Department of Gastrointestinal Surgery, Key Laboratory of Carcinogenesis and Translational Research, Peking University Cancer Hospital, No.52 Fucheng Road Haidian District, Beijing, 100142, People's Republic of China
| | - Linxin Zhou
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research, Peking University Cancer Hospital, No.52 Fucheng Road Haidian District, Beijing, 100142, People's Republic of China
| | - Dongliang Wang
- ChosenMed, Beijing Economic-Technological Development Area, Beijing, 100176, People's Republic of China
| | - Aiwen Wu
- Department of Gastrointestinal Surgery, Key Laboratory of Carcinogenesis and Translational Research, Peking University Cancer Hospital, No.52 Fucheng Road Haidian District, Beijing, 100142, People's Republic of China.
| | - Ziyu Li
- Department of Gastrointestinal Surgery, Key Laboratory of Carcinogenesis and Translational Research, Peking University Cancer Hospital, No.52 Fucheng Road Haidian District, Beijing, 100142, People's Republic of China.
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26
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Kosanke M, Osetek K, Haase A, Wiehlmann L, Davenport C, Schwarzer A, Adams F, Kleppa MJ, Schambach A, Merkert S, Wunderlich S, Menke S, Dorda M, Martin U. Reprogramming enriches for somatic cell clones with small-scale mutations in cancer-associated genes. Mol Ther 2021; 29:2535-2553. [PMID: 33831558 DOI: 10.1016/j.ymthe.2021.04.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 03/03/2021] [Accepted: 04/02/2021] [Indexed: 02/06/2023] Open
Abstract
Cellular therapies based on induced pluripotent stem cells (iPSCs) come out of age and an increasing number of clinical trials applying iPSC-based transplants are ongoing or in preparation. Recent studies, however, demonstrated a high number of small-scale mutations in iPSCs. Although the mutational load in iPSCs seems to be largely derived from their parental cells, it is still unknown whether reprogramming may enrich for individual mutations that could lead to loss of functionality and tumor formation from iPSC derivatives. 30 hiPSC lines were analyzed by whole exome sequencing. High accuracy amplicon sequencing showed that all analyzed small-scale variants pre-existed in their parental cells and that individual mutations present in small subpopulations of parental cells become enriched among hiPSC clones during reprogramming. Among those, putatively actionable driver mutations affect genes related to cell-cycle control, cell death, and pluripotency and may confer a selective advantage during reprogramming. Finally, a short hairpin RNA (shRNA)-based experimental approach was applied to provide additional evidence for the individual impact of such genes on the reprogramming efficiency. In conclusion, we show that enriched mutations in curated onco- and tumor suppressor genes may account for an increased tumor risk and impact the clinical value of patient-derived hiPSCs.
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Affiliation(s)
- Maike Kosanke
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH - Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany, Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research (DZL), 30625 Hannover, Germany
| | - Katarzyna Osetek
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH - Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany, Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research (DZL), 30625 Hannover, Germany
| | - Alexandra Haase
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH - Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany, Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research (DZL), 30625 Hannover, Germany
| | - Lutz Wiehlmann
- Research Core Unit Genomics, Hannover Medical School, 30625 Hannover, Germany
| | - Colin Davenport
- Research Core Unit Genomics, Hannover Medical School, 30625 Hannover, Germany
| | - Adrian Schwarzer
- Department of Hematology, Oncology and Stem Cell Transplantation, Institute of Experimental Hematology, REBIRTH - Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Felix Adams
- Department of Hematology, Oncology and Stem Cell Transplantation, Institute of Experimental Hematology, REBIRTH - Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Marc-Jens Kleppa
- Department of Hematology, Oncology and Stem Cell Transplantation, Institute of Experimental Hematology, REBIRTH - Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Axel Schambach
- Department of Hematology, Oncology and Stem Cell Transplantation, Institute of Experimental Hematology, REBIRTH - Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Sylvia Merkert
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH - Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany, Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research (DZL), 30625 Hannover, Germany
| | - Stephanie Wunderlich
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH - Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany, Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research (DZL), 30625 Hannover, Germany
| | - Sandra Menke
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH - Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany, Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research (DZL), 30625 Hannover, Germany
| | - Marie Dorda
- Research Core Unit Genomics, Hannover Medical School, 30625 Hannover, Germany
| | - Ulrich Martin
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH - Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany, Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research (DZL), 30625 Hannover, Germany.
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Guntur AR, Venkatanarayan A, Gangula S, Lundell MJ. Zfh-2 facilitates Notch-induced apoptosis in the CNS and appendages of Drosophila melanogaster. Dev Biol 2021; 475:65-79. [PMID: 33705738 DOI: 10.1016/j.ydbio.2021.02.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/22/2021] [Accepted: 02/22/2021] [Indexed: 12/26/2022]
Abstract
Apoptosis is a fundamental remodeling process for most tissues during development. In this manuscript we examine a pro-apoptotic function for the Drosophila DNA binding protein Zfh-2 during development of the central nervous system (CNS) and appendages. In the CNS we find that a loss-of-function zfh-2 allele gives an overall reduction of apoptotic cells in the CNS, and an altered pattern of expression for the axonal markers 22C10 and FasII. This same loss-of-function zfh-2 allele causes specific cells in the NB7-3 lineage of the CNS that would normally undergo apoptosis to be inappropriately maintained, whereas a gain-of-function zfh-2 allele has the opposite effect, resulting in a loss of normal NB 7-3 progeny. We also demonstrate that Zfh-2 and Hunchback reciprocally repress each other's gene expression which limits apoptosis to later born progeny of the NB7-3 lineage. Apoptosis is also required for proper segmentation of the fly appendages. We find that Zfh-2 co-localizes with apoptotic cells in the folds of the imaginal discs and presumptive cuticular joints. A reduction of Zfh-2 levels with RNAi inhibits expression of the pro-apoptotic gene reaper, and produces abnormal joints in the leg, antenna and haltere. Apoptosis has previously been shown to be activated by Notch signaling in both the NB7-3 CNS lineage and the appendage joints. Our results indicate that Zfh-2 facilitates Notch-induced apoptosis in these structures.
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Affiliation(s)
- Ananya R Guntur
- Department of Biology, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX, 78249, USA
| | | | - Sindhura Gangula
- Department of Biology, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX, 78249, USA
| | - Martha J Lundell
- Department of Biology, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX, 78249, USA.
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28
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Liu F, Li Y, Ying D, Qiu S, He Y, Li M, Liu Y, Zhang Y, Zhu Q, Hu Y, Liu L, Li G, Pan W, Jin W, Mu J, Cao Y, Liu Y. Whole-exome mutational landscape of neuroendocrine carcinomas of the gallbladder. Signal Transduct Target Ther 2021; 6:55. [PMID: 33563892 PMCID: PMC7873252 DOI: 10.1038/s41392-020-00412-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 10/14/2020] [Accepted: 10/28/2020] [Indexed: 12/23/2022] Open
Abstract
Neuroendocrine carcinoma (NEC) of the gallbladder (GB-NEC) is a rare but extremely malignant subtype of gallbladder cancer (GBC). The genetic and molecular signatures of GB-NEC are poorly understood; thus, molecular targeting is currently unavailable. In the present study, we applied whole-exome sequencing (WES) technology to detect gene mutations and predicted somatic single-nucleotide variants (SNVs) in 15 cases of GB-NEC and 22 cases of general GBC. In 15 GB-NECs, the C > T mutation was predominant among the 6 types of SNVs. TP53 showed the highest mutation frequency (73%, 11/15). Compared with neuroendocrine carcinomas of other organs, significantly mutated genes (SMGs) in GB-NECs were more similar to those in pulmonary large-cell neuroendocrine carcinomas (LCNECs), with driver roles for TP53 and RB1. In the COSMIC database of cancer-related genes, 211 genes were mutated. Strikingly, RB1 (4/15, 27%) and NAB2 (3/15, 20%) mutations were found specifically in GB-NECs; in contrast, mutations in 29 genes, including ERBB2 and ERBB3, were identified exclusively in GBC. Mutations in RB1 and NAB2 were significantly related to downregulation of the RB1 and NAB2 proteins, respectively, according to immunohistochemical (IHC) data (p values = 0.0453 and 0.0303). Clinically actionable genes indicated 23 mutated genes, including ALK, BRCA1, and BRCA2. In addition, potential somatic SNVs predicted by ISOWN and SomVarIUS constituted 6 primary COSMIC mutation signatures (1, 3, 30, 6, 7, and 13) in GB-NEC. Genes carrying somatic SNVs were enriched mainly in oncogenic signaling pathways involving the Notch, WNT, Hippo, and RTK-RAS pathways. In summary, we have systematically identified the mutation landscape of GB-NEC, and these findings may provide mechanistic insights into the specific pathogenesis of this deadly disease.
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Affiliation(s)
- Fatao Liu
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Yangpu District, Shanghai, 200092, China
- Shanghai Key Laboratory of Biliary Tract Disease, Yangpu District, Shanghai, 200092, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai, China
- Shanghai Research Center of Biliary Tract Disease, Yangpu District, Shanghai, 200092, China
| | - Yongsheng Li
- Shanghai Key Laboratory of Biliary Tract Disease, Yangpu District, Shanghai, 200092, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai, China
- Shanghai Research Center of Biliary Tract Disease, Yangpu District, Shanghai, 200092, China
- Department of Biliary-Pancreatic Surgery, Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dongjian Ying
- Department of Minimal Invasive Surgery, Ningbo Medical Center Lihuili Hospital, Ningbo, Zhejiang, 315040, China
| | - Shimei Qiu
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Yangpu District, Shanghai, 200092, China
- Shanghai Key Laboratory of Biliary Tract Disease, Yangpu District, Shanghai, 200092, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai, China
- Shanghai Research Center of Biliary Tract Disease, Yangpu District, Shanghai, 200092, China
| | - Yong He
- Department of hepatopancreatobiliary surgery, Ganzhou hospital affiliated to Nanchang university, Jiangxi, 341000, China
| | - Maolan Li
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Yangpu District, Shanghai, 200092, China
- Shanghai Key Laboratory of Biliary Tract Disease, Yangpu District, Shanghai, 200092, China
- Shanghai Research Center of Biliary Tract Disease, Yangpu District, Shanghai, 200092, China
| | - Yun Liu
- Shanghai Key Laboratory of Biliary Tract Disease, Yangpu District, Shanghai, 200092, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai, China
- Shanghai Research Center of Biliary Tract Disease, Yangpu District, Shanghai, 200092, China
- Department of Biliary-Pancreatic Surgery, Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yijian Zhang
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Yangpu District, Shanghai, 200092, China
- Shanghai Key Laboratory of Biliary Tract Disease, Yangpu District, Shanghai, 200092, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai, China
- Shanghai Research Center of Biliary Tract Disease, Yangpu District, Shanghai, 200092, China
| | - Qin Zhu
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Yangpu District, Shanghai, 200092, China
- Shanghai Key Laboratory of Biliary Tract Disease, Yangpu District, Shanghai, 200092, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai, China
- Shanghai Research Center of Biliary Tract Disease, Yangpu District, Shanghai, 200092, China
| | - Yunping Hu
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Yangpu District, Shanghai, 200092, China
- Shanghai Key Laboratory of Biliary Tract Disease, Yangpu District, Shanghai, 200092, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai, China
- Shanghai Research Center of Biliary Tract Disease, Yangpu District, Shanghai, 200092, China
| | - Liguo Liu
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Yangpu District, Shanghai, 200092, China
- Shanghai Key Laboratory of Biliary Tract Disease, Yangpu District, Shanghai, 200092, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai, China
- Shanghai Research Center of Biliary Tract Disease, Yangpu District, Shanghai, 200092, China
- Department of Biliary-Pancreatic Surgery, Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guoqiang Li
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Yangpu District, Shanghai, 200092, China
- Shanghai Key Laboratory of Biliary Tract Disease, Yangpu District, Shanghai, 200092, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai, China
- Shanghai Research Center of Biliary Tract Disease, Yangpu District, Shanghai, 200092, China
- Department of Biliary-Pancreatic Surgery, Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weihua Pan
- Department of Pediatric Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Yangpu District, Shanghai, 200092, China
- Information and Big Data Center, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Yangpu District, Shanghai, 200092, China
| | - Wei Jin
- Information and Big Data Center, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Yangpu District, Shanghai, 200092, China
| | - Jiasheng Mu
- Department of General Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Yangpu District, Shanghai, 200092, China.
- Information and Big Data Center, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Yangpu District, Shanghai, 200092, China.
| | - Yang Cao
- Department of Surgery, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310009, China.
- Department of Gastric Surgery, Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China.
| | - Yingbin Liu
- Shanghai Key Laboratory of Biliary Tract Disease, Yangpu District, Shanghai, 200092, China.
- State Key Laboratory of Oncogenes and Related Genes, Shanghai, China.
- Shanghai Research Center of Biliary Tract Disease, Yangpu District, Shanghai, 200092, China.
- Department of Biliary-Pancreatic Surgery, Renji Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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29
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Meier T, Timm M, Montani M, Wilkens L. Gene networks and transcriptional regulators associated with liver cancer development and progression. BMC Med Genomics 2021; 14:41. [PMID: 33541355 PMCID: PMC7863452 DOI: 10.1186/s12920-021-00883-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 01/24/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Treatment options for hepatocellular carcinoma (HCC) are limited, and overall survival is poor. Despite the high frequency of this malignoma, its basic disease mechanisms are poorly understood. Therefore, the aim of this study was to use different methodological approaches and combine the results to improve our knowledge on the development and progression of HCC. METHODS Twenty-three HCC samples were characterized by histological, morphometric and cytogenetic analyses, as well as comparative genomic hybridization (aCGH) and genome-wide gene expression followed by a bioinformatic search for potential transcriptional regulators and master regulatory molecules of gene networks. RESULTS Histological evaluation revealed low, intermediate and high-grade HCCs, and gene expression analysis split them into two main sets: GE1-HCC and GE2-HCC, with a low and high proliferation gene expression signature, respectively. Array-based comparative genomic hybridization demonstrated a high level of chromosomal instability, with recurrent chromosomal gains of 1q, 6p, 7q, 8q, 11q, 17q, 19p/q and 20q in both HCC groups and losses of 1p, 4q, 6q, 13q and 18q characteristic for GE2-HCC. Gene expression and bioinformatics analyses revealed that different genes and gene regulatory networks underlie the distinct biological features observed in GE1-HCC and GE2-HCC. Besides previously reported dysregulated genes, the current study identified new candidate genes with a putative role in liver cancer, e.g. C1orf35, PAFAH1B3, ZNF219 and others. CONCLUSION Analysis of our findings, in accordance with the available published data, argues in favour of the notion that the activated E2F1 signalling pathway, which can be responsible for both inappropriate cell proliferation and initial chromosomal instability, plays a pivotal role in HCC development and progression. A dedifferentiation switch that manifests in exaggerated gene expression changes might be due to turning on transcriptional co-regulators with broad impact on gene expression, e.g. POU2F1 (OCT1) and NFY, as a response to accumulating cell stress during malignant development. Our findings point towards the necessity of different approaches for the treatment of HCC forms with low and high proliferation signatures and provide new candidates for developing appropriate HCC therapies.
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Affiliation(s)
- Tatiana Meier
- Institute of Pathology, Nordstadtkrankenhaus, Hanover, Germany.
| | - Max Timm
- Institute of Pathology, Nordstadtkrankenhaus, Hanover, Germany
- Clinic for Laryngology, Rhinology and Otology, Medical School Hanover, Hanover, Germany
| | - Matteo Montani
- Institute of Pathology, University of Bern, Bern, Switzerland
| | - Ludwig Wilkens
- Institute of Pathology, Nordstadtkrankenhaus, Hanover, Germany
- Institute of Human Genetics, Medical School Hanover, Hanover, Germany
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30
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Song Z, Yang L, Zhou Z, Li P, Wang W, Cheng G, Chen R, Chang L, Zhang Y, Guan Y, Xia X, Yi X, Zhou R, Chen M. Genomic profiles and tumor immune microenvironment of primary lung carcinoma and brain oligo-metastasis. Cell Death Dis 2021; 12:106. [PMID: 33479213 PMCID: PMC7820277 DOI: 10.1038/s41419-021-03410-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 12/03/2020] [Accepted: 12/07/2020] [Indexed: 02/07/2023]
Abstract
Brain metastasis (BM) is a common malignant event in lung cancer. Here, we recruited 33 lung cancer patients with brain oligo-metastasis to explore the genomic features and tumor immune microenvironment (TIME) of the lung and BM independently. For genomic profiling, targeted sequencing was performed. We found that high-frequent ZFHX3 occurred in the lung (40%) and brain tumor (28%), which might relate to brain metastasis event; the vast majority of patients had lesions-shared mutations in primary tumor and BM, confirming the common clonal events; and EGFR was the most frequently clonal gene in both lung and BM, indicating its driver capability. To characterize TIME status, we also sequenced the T cell receptor (TCR) repertoires and performed immunohistochemistry (IHC) on CD8+ tumor-infiltrating lymphocytes (TILs) and PD-L1 expression in 28 patients who had paired samples. Through the comparison, the TCR clonality of BM was higher than lung tumor, indicating the distinct pattern of the stronger oligoclonal T cell expansion in BM; the primary tumor had a higher TMB than oligo-BM (13.9 vs 8.7 mutations, p = 0.019); CD8 + TILs of BM were significantly lower than lung tumor (10% vs 30%, p = 0.015), revealing the lower level of cytotoxic T cell infiltration; BM showed statistically equivalent level of PD-L1 compared with lung tumor (p = 0.722). We further investigated the potential biomarkers associated with overall survival (OS) after brain surgery. We found that higher TCR clonality was related to prolonged OS in EGFR-treated patients (HR 0.175, p < 0.001) but the worse outcomes in non-EGFR-treated (HR 2.623, p = 0.034). More CD8+ TILs were an independently positive indicator for OS, in EGFR-treated (HR 0.160, p = 0.001) and non-EGFR-treated patients (HR 0.308, p = 0.009). These findings provide a meaningful molecular and clinical understanding of lung carcinoma and brain oligo-metastasis.
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Affiliation(s)
- Zhengbo Song
- Department of Clinical Trial, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang, 310022, China. .,Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China.
| | - Ling Yang
- Geneplus-Beijing Institute, Beijing, 102206, China
| | - Zhipeng Zhou
- Geneplus-Beijing Institute, Beijing, 102206, China
| | - Pansong Li
- Geneplus-Beijing Institute, Beijing, 102206, China
| | - Wenxian Wang
- Department of Clinical Trial, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang, 310022, China
| | - Guoping Cheng
- Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China.,Department of Pathology, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang, 310022, China
| | | | | | - Yiping Zhang
- Department of Clinical Trial, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang, 310022, China
| | - Yanfang Guan
- Geneplus-Beijing Institute, Beijing, 102206, China
| | - Xuefeng Xia
- Geneplus-Beijing Institute, Beijing, 102206, China
| | - Xin Yi
- Geneplus-Beijing Institute, Beijing, 102206, China
| | - Rongrong Zhou
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
| | - Ming Chen
- Department of Radiotherapy, The Cancer Hospital of the University of Chinese Academy of Science (Zhejiang Cancer Hospital), Hangzhou, Zhejiang, 310022, China.
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31
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Xu A, Huang MF, Zhu D, Gingold JA, Bazer DA, Chang B, Wang D, Lai CC, Lemischka IR, Zhao R, Lee DF. LncRNA H19 Suppresses Osteosarcomagenesis by Regulating snoRNAs and DNA Repair Protein Complexes. Front Genet 2021; 11:611823. [PMID: 33519915 PMCID: PMC7844330 DOI: 10.3389/fgene.2020.611823] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 12/15/2020] [Indexed: 12/26/2022] Open
Abstract
Osteosarcoma is one of the most frequent common primary malignant tumors in childhood and adolescence. Long non-coding RNAs (lncRNAs) have been reported to regulate the initiation and progression of tumors. However, the exact molecular mechanisms involving lncRNA in osteosarcomagenesis remain largely unknown. Li-Fraumeni syndrome (LFS) is a familial cancer syndrome caused by germline p53 mutation. We investigated the tumor suppressor function of lncRNA H19 in LFS-associated osteosarcoma. Analyzing H19-induced transcriptome alterations in LFS induced pluripotent stem cell (iPSC)-derived osteoblasts, we unexpectedly discovered a large group of snoRNAs whose expression was significantly affected by H19. We identified SNORA7A among the H19-suppressed snoRNAs. SNORA7A restoration impairs H19-mediated osteogenesis and tumor suppression, indicating an oncogenic role of SNORA7A. TCGA analysis indicated that SNORA7A expression is associated with activation of oncogenic signaling and poor survival in cancer patients. Using an optimized streptavidin-binding RNA aptamer designed from H19 lncRNA, we revealed that H19-tethered protein complexes include proteins critical for DNA damage response and repair, confirming H19's tumor suppressor role. In summary, our findings demonstrate a critical role of H19-modulated SNORA7A expression in LFS-associated osteosarcomas.
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Affiliation(s)
- An Xu
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Mo-Fan Huang
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Dandan Zhu
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Julian A Gingold
- Department of Obstetrics and Gynecology and Women's Health, Einstein/Montefiore Medical Center, Bronx, NY, United States
| | - Danielle A Bazer
- Department of Neurology, Renaissance School of Medicine at Stony Brook University, Stony Brook, NY, United States
| | - Betty Chang
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Donghui Wang
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Chien-Chen Lai
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan.,Graduate Institute of Chinese Medical Science, China Medical University, Taichung, Taiwan
| | - Ihor R Lemischka
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Ruiying Zhao
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Dung-Fang Lee
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States.,The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States.,Center for Stem Cell and Regenerative Medicine, The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, The University of Texas Health Science Center at Houston, Houston, TX, United States.,Center for Precision Health, School of Biomedical Informatics and School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, United States
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32
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Dong G, Ma G, Wu R, Liu J, Liu M, Gao A, Li X, A J, Liu X, Zhang Z, Zhang B, Fu L, Dong JT. ZFHX3 Promotes the Proliferation and Tumor Growth of ER-Positive Breast Cancer Cells Likely by Enhancing Stem-Like Features and MYC and TBX3 Transcription. Cancers (Basel) 2020; 12:cancers12113415. [PMID: 33217982 PMCID: PMC7698617 DOI: 10.3390/cancers12113415] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/10/2020] [Accepted: 11/12/2020] [Indexed: 12/23/2022] Open
Abstract
Simple Summary Breast cancer is a common malignancy, but the understanding of its cellular and molecular mechanisms is limited. The ZFHX3 transcription factor regulates mammary epithelial cells’ proliferation and differentiation by interacting with estrogen and progesterone receptors. Both these receptors play crucial roles in breast cancer development, but whether ZFHX3 also impacts breast cancer is unknown. In this study, the authors aim to determine if ZFHX3 promotes breast cancer cells’ proliferation and tumor growth and explore the underlying cellular and molecular mechanisms. Higher ZFHX3 expression is associated with worse patient survival in breast cancer, ZFHX3 promotes the proliferation and tumor growth of breast cancer cells, and several breast cancer stem cell factors appear to be involved in the role of ZFHX3 in breast cancer growth. The findings suggest that ZFHX3 is a novel oncogenic molecule promoting breast cancer development. Such a molecule could provide novel opportunities for the treatment of breast cancer. Abstract Breast cancer is a common malignancy, but the understanding of its cellular and molecular mechanisms is limited. ZFHX3, a transcription factor with many homeodomains and zinc fingers, suppresses prostatic carcinogenesis but promotes tumor growth of liver cancer cells. ZFHX3 regulates mammary epithelial cells’ proliferation and differentiation by interacting with estrogen and progesterone receptors, potent breast cancer regulators. However, whether ZFHX3 plays a role in breast carcinogenesis is unknown. Here, we found that ZFHX3 promoted the proliferation and tumor growth of breast cancer cells in culture and nude mice; and higher expression of ZFHX3 in human breast cancer specimens was associated with poorer prognosis. The knockdown of ZFHX3 in ZFHX3-high MCF-7 cells decreased, and ZFHX3 overexpression in ZFHX3-low T-47D cells increased the proportion of breast cancer stem cells (BCSCs) defined by mammosphere formation and the expression of CD44, CD24, and/or aldehyde dehydrogenase 1. Among several transcription factors that have been implicated in BCSCs, MYC and TBX3 were transcriptionally activated by ZFHX3 via promoter binding, as demonstrated by luciferase-reporter and ChIP assays. These findings suggest that ZFHX3 promotes breast cancer cells’ proliferation and tumor growth likely by enhancing BCSC features and upregulating MYC, TBX3, and others.
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Affiliation(s)
- Ge Dong
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China; (G.D.); (G.M.); (J.L.); (M.L.); (A.G.); (X.L.); (J.A.); (L.F.)
| | - Gui Ma
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China; (G.D.); (G.M.); (J.L.); (M.L.); (A.G.); (X.L.); (J.A.); (L.F.)
| | - Rui Wu
- Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Blvd, Shenzhen 518055, China; (R.W.); (X.L.); (Z.Z.)
| | - Jinming Liu
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China; (G.D.); (G.M.); (J.L.); (M.L.); (A.G.); (X.L.); (J.A.); (L.F.)
| | - Mingcheng Liu
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China; (G.D.); (G.M.); (J.L.); (M.L.); (A.G.); (X.L.); (J.A.); (L.F.)
- Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Blvd, Shenzhen 518055, China; (R.W.); (X.L.); (Z.Z.)
| | - Ang Gao
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China; (G.D.); (G.M.); (J.L.); (M.L.); (A.G.); (X.L.); (J.A.); (L.F.)
| | - Xiawei Li
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China; (G.D.); (G.M.); (J.L.); (M.L.); (A.G.); (X.L.); (J.A.); (L.F.)
- Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Blvd, Shenzhen 518055, China; (R.W.); (X.L.); (Z.Z.)
| | - Jun A
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China; (G.D.); (G.M.); (J.L.); (M.L.); (A.G.); (X.L.); (J.A.); (L.F.)
- Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Blvd, Shenzhen 518055, China; (R.W.); (X.L.); (Z.Z.)
| | - Xiaoyu Liu
- Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Blvd, Shenzhen 518055, China; (R.W.); (X.L.); (Z.Z.)
| | - Zhiqian Zhang
- Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Blvd, Shenzhen 518055, China; (R.W.); (X.L.); (Z.Z.)
| | - Baotong Zhang
- Emory Winship Cancer Institute, Department of Hematology and Medical Oncology, Emory University School of Medicine, 1365-C Clifton Road, Atlanta, GA 30322, USA;
| | - Liya Fu
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China; (G.D.); (G.M.); (J.L.); (M.L.); (A.G.); (X.L.); (J.A.); (L.F.)
| | - Jin-Tang Dong
- Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Blvd, Shenzhen 518055, China; (R.W.); (X.L.); (Z.Z.)
- Correspondence:
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Li C, Chen Q, Zhou Y, Niu Y, Wang X, Li X, Zheng H, Wei T, Zhao L, Gao H. S100A2 promotes glycolysis and proliferation via GLUT1 regulation in colorectal cancer. FASEB J 2020; 34:13333-13344. [PMID: 32816365 DOI: 10.1096/fj.202000555r] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 07/16/2020] [Accepted: 07/19/2020] [Indexed: 01/05/2023]
Abstract
The deregulation of S100A2 has been implicated in the pathogenesis of several types of cancers. However, the molecular mechanisms underlying the protumorigenic capacities of S100A2 have not been fully elucidated. Here, we demonstrated the molecular mechanisms underlying the roles of S100A2 in glycolysis reprogramming and proliferation of colorectal cancer (CRC) cells. The results indicated that S100A2 overexpression raises glucose metabolism and proliferation. Mechanistically, S100A2 activated the PI3K/AKT signaling pathway, upregulated GLUT1 expression, induced glycolytic reprogramming, and consequently increased proliferation. Clinical data showed significantly increased S100A2 levels in CRC tissues and the Oncomine database. In addition, analysis revealed a positive correlation between S100A2 and GLUT1 mRNA expression in CRC tissues. Together, these results demonstrate that the S100A2/GLUT1 axis can promote the progression of CRC by modulating glycolytic reprogramming. Our results further suggest that targeting S100A2 could present a promising therapeutic avenue for the prevention of colorectal cancer progression.
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Affiliation(s)
- Chen Li
- Institute of Metabonomics & Medical NMR, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Qinbo Chen
- Institute of Metabonomics & Medical NMR, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Yi Zhou
- Institute of Metabonomics & Medical NMR, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Yan Niu
- Institute of Metabonomics & Medical NMR, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xinyi Wang
- Institute of Metabonomics & Medical NMR, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xiang Li
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou, China.,School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Hong Zheng
- Institute of Metabonomics & Medical NMR, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Tingting Wei
- Institute of Metabonomics & Medical NMR, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Liangcai Zhao
- Institute of Metabonomics & Medical NMR, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Hongchang Gao
- Institute of Metabonomics & Medical NMR, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
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Lee SY, Chae DK, Lee SH, Lim Y, An J, Chae CH, Kim BC, Bhak J, Bolser D, Cho DH. Efficient mutation screening for cervical cancers from circulating tumor DNA in blood. BMC Cancer 2020; 20:694. [PMID: 32718341 PMCID: PMC7385901 DOI: 10.1186/s12885-020-07161-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 07/09/2020] [Indexed: 12/13/2022] Open
Abstract
Background Early diagnosis and continuous monitoring are necessary for an efficient management of cervical cancers (CC). Liquid biopsy, such as detecting circulating tumor DNA (ctDNA) from blood, is a simple, non-invasive method for testing and monitoring cancer markers. However, tumor-specific alterations in ctDNA have not been extensively investigated or compared to other circulating biomarkers in the diagnosis and monitoring of the CC. Therfore, Next-generation sequencing (NGS) analysis with blood samples can be a new approach for highly accurate diagnosis and monitoring of the CC. Method Using a bioinformatics approach, we designed a panel of 24 genes associated with CC to detect and characterize patterns of somatic single-nucleotide variations, indels, and copy number variations. Our NGS CC panel covers most of the genes in The Cancer Genome Atlas (TCGA) as well as additional cancer driver and tumor suppressor genes. We profiled the variants in ctDNA from 24 CC patients who were being treated with systemic chemotherapy and local radiotherapy at the Jeonbuk National University Hospital, Korea. Result Eighteen out of 24 genes in our NGS CC panel had mutations across the 24 CC patients, including somatic alterations of mutated genes (ZFHX3–83%, KMT2C-79%, KMT2D-79%, NSD1–67%, ATM-38% and RNF213–27%). We demonstrated that the RNF213 mutation could be used potentially used as a monitoring marker for response to chemo- and radiotherapy. Conclusion We developed our NGS CC panel and demostrated that our NGS panel can be useful for the diagnosis and monitoring of the CC, since the panel detected the common somatic variations in CC patients and we observed how these genetic variations change according to the treatment pattern of the patient.
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Affiliation(s)
- Sun-Young Lee
- Department of Radiation Oncology, Jeonbuk National University Hospital-Jeonbuk National University Medical School, Jeonju, Jeonbuk, Republic of Korea.,Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, Republic of Korea
| | | | | | - Yohan Lim
- Clinomics Inc, Suwon, 16229, Republic of Korea
| | - Jahyun An
- Clinomics Inc, Suwon, 16229, Republic of Korea
| | - Chang Hoon Chae
- Department of Biophysics and Radiation Biology, Lab of Nanochemistry, Semmelweis University, Budapest, Hungary
| | | | - Jong Bhak
- Clinomics Inc, Suwon, 16229, Republic of Korea.,KOGIC, UNIST, Ulsan, 44919, Republic of Korea.,Geromics LTD, Cambridge, CB1 1AH, UK
| | | | - Dong-Hyu Cho
- Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, Republic of Korea. .,Department of Obstetrics and Gynecology, Jeonbuk National University Hospital-Jeonbuk National University Medical School, Jeonju, Jeonbuk, Republic of Korea.
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Liu J, Mei J, Li S, Wu Z, Zhang Y. Establishment of a novel cell cycle-related prognostic signature predicting prognosis in patients with endometrial cancer. Cancer Cell Int 2020; 20:329. [PMID: 32699528 PMCID: PMC7372883 DOI: 10.1186/s12935-020-01428-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 07/15/2020] [Indexed: 12/26/2022] Open
Abstract
Background Endometrial cancer (EnCa) ranks fourth in menace within women’s malignant tumors. Large numbers of studies have proven that functional genes can change the process of tumors by regulating the cell cycle, thereby achieving the goal of targeted therapy. Methods The transcriptional data of EnCa samples obtained from the TCGA database was analyzed. A battery of bioinformatics strategies, which included GSEA, Cox and LASSO regression analysis, establishment of a prognostic signature and a nomogram for overall survival (OS) assessment. The GEPIA and CPTAC analysis were applied to validate the dysregulation of hub genes. For mutation analysis, the “maftools” package was used. Results GSEA identified that cell cycle was the most associated pathway to EnCa. Five cell cycle-related genes including HMGB3, EZH2, NOTCH2, UCK2 and ODF2 were identified as prognosis-related genes to build a prognostic signature. Based on this model, the EnCa patients could be divided into low- and high-risk groups, and patients with high-risk score exhibited poorer OS. Time-dependent ROC and Cox regression analyses revealed that the 5-gene signature could predict EnCa prognosis exactly and independently. GEPIA and CPTAC validation exhibited that these genes were notably dysregulated between EnCa and normal tissues. Lower mutation rates of PTEN, TTN, ARID1A, and etc. were found in samples with high-risk score compared with that with low-risk score. GSEA analysis suggested that the samples of the low- and high-risk groups were concentrated on various pathways, which accounted for the different oncogenic mechanisms in patients in two groups. Conclusion The current research construct a 5-gene signature to evaluate prognosis of EnCa patients, which may innovative clinical application of prognostic assessment.
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Affiliation(s)
- Jinhui Liu
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029 Jiangsu China
| | - Jie Mei
- Department of Oncology, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, 214023 Jiangsu China
| | - Siyue Li
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029 Jiangsu China
| | - Zhipeng Wu
- Department of Urology, The Affiliated Sir Run Run Hospital of Nanjing Medical University, Nanjing, 211166 China
| | - Yan Zhang
- Department of Gynecology and Obstetrics, Wuxi Maternal and Child Health Hospital Affiliated to Nanjing Medical University, No. 48, Huaishu Road, Wuxi, 214000 Jiangsu China
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Zhang J, Zhou N, Lin A, Luo P, Chen X, Deng H, Kang S, Guo L, Zhu W, Zhang J. ZFHX3 mutation as a protective biomarker for immune checkpoint blockade in non-small cell lung cancer. Cancer Immunol Immunother 2020; 70:137-151. [PMID: 32653938 DOI: 10.1007/s00262-020-02668-8] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 07/08/2020] [Indexed: 01/03/2023]
Abstract
To date, immunotherapy has opened a new chapter in the treatment of lung cancer. Precise biomarkers can help to screen subpopulations of lung cancer to provide the best treatment. Multiple studies suggest that specific gene mutations may be predictive markers in guiding non-small cell lung cancer (NSCLC) immune checkpoint inhibitor (ICI) treatment. A published immunotherapy cohort with mutational and survival data for 350 NSCLC patients was used. First, the mutational data of the immunotherapy cohort were used to identify gene mutations related to the prognosis of ICI therapy. The immunotherapy cohort and TCGA-NSCLC cohort were further studied to elucidate the relationships between specific gene mutations and tumor immunogenicity, antitumor immune response capabilities, and immune cell and mutation counts in the DNA damage response (DDR) pathway. In the immunotherapy cohort (N = 350), ZFHX3 mutations were an independent predictive biomarker for NSCLC patients receiving ICI treatment. Significant differences were observed between ZFHX3-mutant (ZFHX3-MT) and ZFHX3-wild type (ZFHX3-WT) patients regarding the overall survival (OS) time (P < 0.001, HR = 0.26, 95% Cl 0.17-0.41). ZFHX3-MT is significantly associated with higher tumor mutation burden (TMB) and neoantigen load (NAL), and ZFHX3-MT positively correlates with known immunotherapy response biomarkers, including T-cell infiltration, immune-related gene expression, and mutation counts in the DDR pathway in NSCLC. ZFHX3-MT is closely related to longer OS in NSCLC patients treated with ICIs, suggesting that ZFHX3 mutations be used as a novel predictive marker in guiding NSCLC ICI treatment.
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Affiliation(s)
- Jiexia Zhang
- National Clinical Research Center for Respiratory Disease, State Key Laboratory of Respiratory Disease, Department of Medicine, Guangzhou Institute of Respiratory Disease, 151 Yanjiang Road, Guangzhou, 510120, Guangdong Province, People's Republic of China
| | - Ningning Zhou
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Anqi Lin
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Gongye Road, Guangzhou, 510282, People's Republic of China
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Gongye Road, Guangzhou, 510282, People's Republic of China
| | - Xin Chen
- Department of Pulmonary and Critical Care Medicine, Zhujiang Hospital, Southern Medical University, 253 Gongye Road, Guangzhou, 510282, People's Republic of China
| | - Huojin Deng
- Department of Pulmonary and Critical Care Medicine, Zhujiang Hospital, Southern Medical University, 253 Gongye Road, Guangzhou, 510282, People's Republic of China
| | - Shijun Kang
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Linlang Guo
- Department of Pathology, Zhujiang Hospital, Southern Medical University, 253 Gongye Road, Guangzhou, 510282, People's Republic of China.
| | - Weiliang Zhu
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Gongye Road, Guangzhou, 510282, People's Republic of China.
| | - Jian Zhang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, 253 Gongye Road, Guangzhou, 510282, People's Republic of China.
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Fu C, An N, Liu J, A J, Zhang B, Liu M, Zhang Z, Fu L, Tian X, Wang D, Dong JT. The transcription factor ZFHX3 is crucial for the angiogenic function of hypoxia-inducible factor 1α in liver cancer cells. J Biol Chem 2020; 295:7060-7074. [PMID: 32277050 DOI: 10.1074/jbc.ra119.012131] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 04/03/2020] [Indexed: 12/15/2022] Open
Abstract
Angiogenesis is a hallmark of tumorigenesis, and hepatocellular carcinoma (HCC) is hypervascular and therefore very dependent on angiogenesis for tumor development and progression. Findings from previous studies suggest that in HCC cells, hypoxia-induced factor 1α (HIF1A) and zinc finger homeobox 3 (ZFHX3) transcription factors functionally interact in the regulation of genes in HCC cells. Here, we report that hypoxia increases the transcription of the ZFHX3 gene and enhances the binding of HIF1A to the ZFHX3 promoter in the HCC cell lines HepG2 and Huh-7. Moreover, ZFHX3, in turn, physically associated with and was functionally indispensable for HIF1A to exert its angiogenic activity, as indicated by in vitro migration and tube formation assays of human umbilical vein endothelial cells (HUVECs) and microvessel formation in xenograft tumors of HCC cells. Mechanistically, ZFHX3 was required for HIF1A to transcriptionally activate the vascular endothelial growth factor A (VEGFA) gene by binding to its promoter. Functionally, down-regulation of ZFHX3 in HCC cells slowed their tumor growth, and addition of VEGFA to conditioned medium from ZFHX3-silenced HCC cells partially rescued the inhibitory effect of this medium on HUVEC tube formation. In human HCC, ZFHX3 expression was up-regulated, and this up-regulation correlated with both HIF1A up-regulation and worse patient survival, confirming a functional association between ZFHX3 and HIF1A in human HCC. We conclude that ZFHX3 is an angiogenic transcription factor that is integral to the HIF1A/VEGFA signaling axis in HCC cells.
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Affiliation(s)
- Changying Fu
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China.,School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen, Guangdong 518055, China
| | - Na An
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China.,School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen, Guangdong 518055, China
| | - Jinming Liu
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Jun A
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China.,School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen, Guangdong 518055, China
| | - Baotong Zhang
- Winship Cancer Institute, Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Mingcheng Liu
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China.,School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen, Guangdong 518055, China
| | - Zhiqian Zhang
- School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen, Guangdong 518055, China
| | - Liya Fu
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Xinxin Tian
- School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen, Guangdong 518055, China
| | - Dan Wang
- School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen, Guangdong 518055, China
| | - Jin-Tang Dong
- School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen, Guangdong 518055, China
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Wu R, Fang J, Liu M, A J, Liu J, Chen W, Li J, Ma G, Zhang Z, Zhang B, Fu L, Dong JT. SUMOylation of the transcription factor ZFHX3 at Lys-2806 requires SAE1, UBC9, and PIAS2 and enhances its stability and function in cell proliferation. J Biol Chem 2020; 295:6741-6753. [PMID: 32249212 DOI: 10.1074/jbc.ra119.012338] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 04/01/2020] [Indexed: 01/07/2023] Open
Abstract
SUMOylation is a posttranslational modification (PTM) at a lysine residue and is crucial for the proper functions of many proteins, particularly of transcription factors, in various biological processes. Zinc finger homeobox 3 (ZFHX3), also known as AT motif-binding factor 1 (ATBF1), is a large transcription factor that is active in multiple pathological processes, including atrial fibrillation and carcinogenesis, and in circadian regulation and development. We have previously demonstrated that ZFHX3 is SUMOylated at three or more lysine residues. Here, we investigated which enzymes regulate ZFHX3 SUMOylation and whether SUMOylation modulates ZFHX3 stability and function. We found that SUMO1, SUMO2, and SUMO3 each are conjugated to ZFHX3. Multiple lysine residues in ZFHX3 were SUMOylated, but Lys-2806 was the major SUMOylation site, and we also found that it is highly conserved among ZFHX3 orthologs from different animal species. Using molecular analyses, we identified the enzymes that mediate ZFHX3 SUMOylation; these included SUMO1-activating enzyme subunit 1 (SAE1), an E1-activating enzyme; SUMO-conjugating enzyme UBC9 (UBC9), an E2-conjugating enzyme; and protein inhibitor of activated STAT2 (PIAS2), an E3 ligase. Multiple analyses established that both SUMO-specific peptidase 1 (SENP1) and SENP2 deSUMOylate ZFHX3. SUMOylation at Lys-2806 enhanced ZFHX3 stability by interfering with its ubiquitination and proteasomal degradation. Functionally, Lys-2806 SUMOylation enabled ZFHX3-mediated cell proliferation and xenograft tumor growth of the MDA-MB-231 breast cancer cell line. These findings reveal the enzymes involved in, and the functional consequences of, ZFHX3 SUMOylation, insights that may help shed light on ZFHX3's roles in various cellular and pathophysiological processes.
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Affiliation(s)
- Rui Wu
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Jiali Fang
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Mingcheng Liu
- School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Jun A
- School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Jinming Liu
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Wenxuan Chen
- School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Juan Li
- School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Gui Ma
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Zhiqian Zhang
- School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Baotong Zhang
- Emory Winship Cancer Institute, Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Liya Fu
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Jin-Tang Dong
- School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
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Lafront C, Germain L, Weidmann C, Audet-Walsh É. A Systematic Study of the Impact of Estrogens and Selective Estrogen Receptor Modulators on Prostate Cancer Cell Proliferation. Sci Rep 2020; 10:4024. [PMID: 32132580 PMCID: PMC7055213 DOI: 10.1038/s41598-020-60844-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 02/17/2020] [Indexed: 01/10/2023] Open
Abstract
The estrogen signaling pathway has been reported to modulate prostate cancer (PCa) progression through the activity of estrogen receptors α and β (ERα and ERβ). Given that selective estrogen receptor modulators (SERMs) are used to treat breast cancer, ERs have been proposed as attractive therapeutic targets in PCa. However, many inconsistencies regarding the expression of ERs and the efficacy of SERMs for PCa treatment exist, notably due to the use of ERβ antibodies lacking specificity and treatments with high SERM concentrations leading to off-target effects. To end this confusion, our objective was to study the impact of estrogenic and anti-estrogenic ligands in well-studied in vitro PCa models with appropriate controls, dosages, and ER subtype-specific antibodies. When using physiologically relevant concentrations of nine estrogenic/anti-estrogenic compounds, including five SERMs, we observed no significant modulation of PCa cell proliferation. Using RNA-seq and validated antibodies, we demonstrate that these PCa models do not express ERs. In contrast, RNA-seq from PCa samples from patients have detectable expression of ERα. Overall, our study reveals that commonly used PCa models are inappropriate to study ERs and indicate that usage of alternative models is essential to properly assess the roles of the estrogen signaling pathway in PCa.
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Affiliation(s)
- Camille Lafront
- Department of molecular medicine, Faculty of Medicine, Université Laval, Québec City, G1V 0A6, Canada
- Endocrinology - Nephrology Research Axis, Centre de recherche du CHU de Québec - Université Laval, Québec City, Canada
- Centre de recherche sur le cancer (CRC) of Université Laval, Québec City, Canada
| | - Lucas Germain
- Endocrinology - Nephrology Research Axis, Centre de recherche du CHU de Québec - Université Laval, Québec City, Canada
- Centre de recherche sur le cancer (CRC) of Université Laval, Québec City, Canada
- Department of biochemistry, microbiology and bioinformatics, Faculty of Sciences and Engineering, Université Laval, Québec City, G1V 0A6, Canada
| | - Cindy Weidmann
- Endocrinology - Nephrology Research Axis, Centre de recherche du CHU de Québec - Université Laval, Québec City, Canada
- Centre de recherche sur le cancer (CRC) of Université Laval, Québec City, Canada
| | - Étienne Audet-Walsh
- Department of molecular medicine, Faculty of Medicine, Université Laval, Québec City, G1V 0A6, Canada.
- Endocrinology - Nephrology Research Axis, Centre de recherche du CHU de Québec - Université Laval, Québec City, Canada.
- Centre de recherche sur le cancer (CRC) of Université Laval, Québec City, Canada.
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Dong Y, Gong W, Hua Z, Chen B, Zhao G, Liu Z, Thiele CJ, Li Z. Combination of Rapamycin and MK-2206 Induced Cell Death via Autophagy and Necroptosis in MYCN-Amplified Neuroblastoma Cell Lines. Front Pharmacol 2020; 11:31. [PMID: 32116708 PMCID: PMC7033642 DOI: 10.3389/fphar.2020.00031] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 01/13/2020] [Indexed: 12/29/2022] Open
Abstract
Neuroblastoma (NB) is the most common pediatric malignant extracranial solid tumor. Despite multi-modality therapies, the emergence of drug resistance is an obstacle in the treatment of high-risk NB patients (with MYCN amplification). In our previous study, we found that rapamycin and MK-2206 synergistically induced cell death in MYCN-amplified cell lines but the mechanisms remained unclear. In our present study, either 3-MA or necroatatin-1 blocked the cell death induced by rapamycin and MK-2206, but z-VAD-fmk did not block this cell death. The expressions of autophagy markers (ATG5, ATG7, Beclin-1, LC3 B) and the necroptosis marker RIPK3 increased and another necroptosis marker RIPK1 decreased after the combination treatment of rapamycin and MK-2206, and were accompanied by the morphological characteristics of autophagy and necroptosis. In NB xenograft tumor tissues, the expressions of autophagy and necroptosis markers were consistent with observations in vitro. These data suggested that autophagy and necroptosis contributed to the cell death induced by rapamycin and MK-2206 in NB cells. To understand the role of MYCN in this process, MYCN expression was downregulated in MYCN-amplified cell lines (NGP, BE2) using siRNAs and was upregulated in MYCN non-amplified cell lines (AS, SY5Y) using plasmid. We found the cell death induced by rapamycin and MK-2206 was MYCN-dependent. We also found that the metabolic activity in NB cells was correlated with the expression level of MYCN. This study delineates the role of MYCN in the cell death induced by combination treatment of rapamycin and MK-2206 in MYCN-amplified NB cells.
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Affiliation(s)
- Yudi Dong
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China.,Medical Research Center, Liaoning Key Laboratory of Research and Application of Animal Models for Environmental and Metabolic Diseases, Shengjing Hospital of China Medical University, Shenyang, China
| | - Wei Gong
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China.,Medical Research Center, Liaoning Key Laboratory of Research and Application of Animal Models for Environmental and Metabolic Diseases, Shengjing Hospital of China Medical University, Shenyang, China
| | - Zhongyan Hua
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China.,Medical Research Center, Liaoning Key Laboratory of Research and Application of Animal Models for Environmental and Metabolic Diseases, Shengjing Hospital of China Medical University, Shenyang, China
| | - Bo Chen
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China.,Medical Research Center, Liaoning Key Laboratory of Research and Application of Animal Models for Environmental and Metabolic Diseases, Shengjing Hospital of China Medical University, Shenyang, China
| | - Guifeng Zhao
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China.,Medical Research Center, Liaoning Key Laboratory of Research and Application of Animal Models for Environmental and Metabolic Diseases, Shengjing Hospital of China Medical University, Shenyang, China
| | - Zhihui Liu
- Cellular & Molecular Biology Section, Pediatric Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Carol J Thiele
- Cellular & Molecular Biology Section, Pediatric Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Zhijie Li
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China.,Medical Research Center, Liaoning Key Laboratory of Research and Application of Animal Models for Environmental and Metabolic Diseases, Shengjing Hospital of China Medical University, Shenyang, China
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Laera L, Guaragnella N, Giannattasio S, Moro L. 6-Thioguanine and Its Analogs Promote Apoptosis of Castration-Resistant Prostate Cancer Cells in a BRCA2-Dependent Manner. Cancers (Basel) 2019; 11:E945. [PMID: 31284411 PMCID: PMC6678799 DOI: 10.3390/cancers11070945] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 07/03/2019] [Indexed: 12/27/2022] Open
Abstract
Background: Mutations in the oncosuppressor gene BReast CAncer susceptibility gene 2 (BRCA2) predispose to aggressive forms of prostate cancer which show poor response to taxane-based therapy, the standard treatment for castration-resistant, aggressive prostate cancer. Herein, we addressed the question whether changes in BRCA2 expression, a potential surrogate marker for BRCA2 activity, may affect the response of castration-resistant prostate cancer cells to 6-thioguanine (6-TG), a thiopurine used in the treatment of haematological malignancies. Methods: Yeast, normal prostate cells and castration-resistant prostate cancer cells were treated with 6-TG or its analogues, in presence or absence of paclitaxel, or with olaparib, a poly-(ADP-ribose) polymerase (PARP) inhibitor currently in clinical trials for treatment of metastatic castration-resistant prostate cancer, and cell proliferation, apoptosis and androgen receptor (AR) levels were measured. Results: 6-TG inhibited cell proliferation in yeast, normal and castration-resistant prostate cancer cells but promoted apoptosis only in cancer cells. Suppression of BRCA2 expression by siRNA or shRNA increased the sensitivity to 6-TG- and olaparib-induced apoptosis but did not affect cancer cell response to taxane. Intriguingly, 6-TG reduced AR expression levels independently on BRCA2 expression. Instead, olaparib decreased AR levels only in BRCA2-knockdown prostate cancer cells. Notably, overexpression of BRCA2 resulted in resistance of castration-resistant prostate cancer cells to 6-TG-, taxane- and olaparib-based treatment but promoted sensitivity to apoptosis induced by 2-amino-6-bromopurine and 2,6-dithiopurine, two 6-TG analogues. Conclusions: Our results provide a pre-clinical rationale for the use of 6-TG in the treatment of BRCA2-deficient castration-resistant prostate cancers, and of certain 6-TG analogues for treatment of BRCA2-proficient prostate cancers.
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Affiliation(s)
- Luna Laera
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Via Amendola 122/O, 70126 Bari, Italy
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Via Orabona 4, 70125 Bari, Italy
| | - Nicoletta Guaragnella
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Via Amendola 122/O, 70126 Bari, Italy
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Via Orabona 4, 70125 Bari, Italy
| | - Sergio Giannattasio
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Via Amendola 122/O, 70126 Bari, Italy
| | - Loredana Moro
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Via Amendola 122/O, 70126 Bari, Italy.
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Ma G, Gao A, Yang Y, He Y, Zhang X, Zhang B, Zhang Z, Li M, Fu X, Zhao D, Wu R, Qi L, Hu Q, Li J, Fu L, Zhu Z, Dong JT. Zfhx3 is essential for progesterone/progesterone receptor signaling to drive ductal side-branching and alveologenesis in mouse mammary glands. J Genet Genomics 2019; 46:119-131. [PMID: 30954439 DOI: 10.1016/j.jgg.2019.03.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 03/05/2019] [Indexed: 01/26/2023]
Abstract
Progesterone (Pg)/progesterone receptor (PR) signaling drives mammary gland side-branching and alveologenesis, but the mechanisms through which Pg/PR signaling functions remain to be clarified. Using in vitro and in vivo models and histological and molecular analyses, we determined the role of Zfhx3 transcription factor in mammary gland development driven by Pg/PR signaling. Postnatal deletion of Zfhx3 in mouse mammary epithelial cells attenuated side-branching morphogenesis and alveologenesis. These effects were undetectable in the absence of Pg/PR signaling. During the estrus cycle, Zfhx3 expression corresponded to that of Pg, being at the highest level at the diestrus stage; Zfhx3 deletion inhibited mammary gland branching more potently at diestrus than estrus stage. Loss of Zfhx3 not only attenuated the expansion of stem/progenitor cells driven by Pg/PR signaling, but also impaired the function of Pg/PR signaling in the transcriptional activation of multiple genes. In addition, Pg/PR signaling significantly expanded PR- and Zfhx3-positive epithelial cells, and induced the physical association of ZFHX3 with PR. These findings establish Zfhx3 as an integral transcription factor of Pg/PR signaling in driving side-branching and alveologenesis during mammary gland development.
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Affiliation(s)
- Gui Ma
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Ang Gao
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Yinan Yang
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Yuan He
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Xi Zhang
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Baotong Zhang
- Department of Hematology and Medical Oncology, School of Medicine, Winship Cancer Institute, Emory University, Atlanta, GA, 30322, USA
| | - Zhiqian Zhang
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Mei Li
- Ningbo Institute of Medical Sciences, Ningbo, 315020, China
| | - Xing Fu
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Dan Zhao
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Rui Wu
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Leilei Qi
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Qingxia Hu
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Juan Li
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Liya Fu
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Zhengmao Zhu
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Jin-Tang Dong
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China; Department of Hematology and Medical Oncology, School of Medicine, Winship Cancer Institute, Emory University, Atlanta, GA, 30322, USA.
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