YY1 in the Control of the Pathogenesis and Drug Resistance of Cancer: A Critical Therapeutic Target

YY1 in the Control of the Pathogenesis and Drug Resistance of Cancer

A Critical Therapeutic Target

First Edition

Benjamin Bonavida

Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, United States

Table of Contents

Cover image

Title page

Copyright

Aims and Scope

About the Editor

Preface

Contributors

Section I: General properties of YY1 in cancer

Chapter 1: The structure of Yin Yang 1 protein and its importance in the interaction with molecular partners

Abstract

Conflict of interest

Evolutionary conservation of Yin Yang 1

Structure of human YY1

Interaction with DNA

Interaction with RNA

Interaction with other proteins

Modulation of YY1 activity

Conclusion

Chapter 2: YY1 and noncoding RNAs: A two-way relationship

Abstract

Conflict of interest

Introduction

ncRNAs and their involvement in cancer

YY1 features and functions

YY1 and ncRNAs

YY1, ncRNAs, and cancer

Conclusions and future perspective

Chapter 3: YY1 regulation of the cancer stem cell phenotype

Abstract

Acknowledgments

Conflict of interest

Introduction

Cancer stem cells

YY1 is needed in normal stem cells

YY1-mediated functions associated with differentiation potential in normal stem cells

Brain tumors

Breast cancer

Liver tumors

Endometrial cancer

Melanoma

Conclusions and perspectives

Chapter 4: YY1 involvement in embryonic development and cancer

Abstract

Conflict of interest

Introduction

Development, carcinogenesis, and Ying Yang 1

To be or not to be, where to be, that is the question: The cell’s fate is controlled by the pioneer transcription factor YY1 in embryonic development

YY1 expression in stem cells and cancer stem cells: Current status and clinical implications

Conclusion

Chapter 5: Yin and Yang of YY1 regulation on tumor metabolic reprogramming

Abstract

Acknowledgments

Conflict of interest

Tumor metabolism

Introduction to Yin Yang 1

YY1 and catabolism

YY1 and anabolism

YY1 and mitochondrial biogenesis

YY1 and anticancer drugs resistance

Conclusion and perspective

Chapter 6: YY1 and tumor metastasis regulation

Abstract

Acknowledgments

Conflict of interest

Introduction

YY1 and EMT

YY1 and angiogenesis

YY1 and metastatic colonization

Crosstalk between YY1-mediated metastasis and other tumor characteristics

Conclusions

Section II: Expression of YY1 in cancers and prognoses

Chapter 7: Molecular mechanisms of YY1 overexpression in human cancers and its prognostic significance

Abstract

Acknowledgments

Conflict of interest

Introduction on prognostic markers

The molecular role of YY1 and the importance of cellular context

YY1 as a prognostic marker in tumors

Mechanisms of YY1 overexpression in cancer

Mechanisms through which YY1 can behave both as oncogene and tumor suppressor: A lesson from breast cancer

Conclusive remarks and future directions

Chapter 8: YY1 is involved in the pathogenesis and malignant properties of human triple-negative breast cancer (TNBC)

Abstract

Acknowledgments

Conflict of interest

Introduction

YY1 regulation of miRNAs in TNBC

The NF-κB/YY1/Snail/RKIP/PTEN loop in TNBC

The YY1/LINC00152/PTEN axis

The mtp53/PARP1/YY1 axis

YY1 regulation of FEN1 in TNBC

YY1 regulation of BRCA in TNBC

Discussion

Chapter 9: YY1 is a potential key player in the pathogenesis of malignant melanoma

Abstract

Conflict of interest

Introduction

Clinical presentation and classification of malignant melanoma

Staging of malignant melanoma

The role of BRAF mutation in melanoma pathogenesis

Melanoma evades and inhibits immune responses

The role of transcription factors

The role of YY1 in melanoma

Conclusion

Chapter 10: Participation of different miRNAs in the regulation of YY1: Their role in pathogenesis, chemoresistance, and therapeutic implication in hematologic malignancies

Abstract

Conflict of interest

Introduction

YY1 in hematological malignancies

miRNAs in hematological malignancies

miRNAs in leukemias (leukemiRs)

miRNAs in the regulation of YY1

Roles of miRNAs and YY1 in the pathogenesis of hematological malignancies

New therapies and the participation of miRNAs and YY1

Conclusions

Chapter 11: Role, regulatory mechanism and clinical correlation of YY1 in HCC

Abstract

Conflict of interest

Introduction

Roles of YY1 in the malignant phenotypes of HCC

The regulatory mechanism of YY1 in the development of HCC

Clinical correlation between YY1 and HCC

Conclusion

Section III: YY1 and drug resistance

Chapter 12: Targeting YY1 in cancer through histone acetylation

Abstract

Conflict of interest

Introduction

YY1 functional domains

Role of histone acetylation in cancer

YY1 is a loop-mediating factor involved in enhancer-promoter interactions

BET bromodomains inhibitors

CREBBP/EP300 bromodomain inhibitors

HDACs inhibitors

Perspectives

Chapter 13: The role of YY1 in drug resistant cancer: Involvement of the YY1/PTEN/PP2A/H2Ax/Rad51 axis

Abstract

Acknowledgments

Conflict of interest

Introduction

YY1: General properties and functions

Role of YY1 in protecting DNA damage

Discussion

Future perspectives

Chapter 14: Chemotherapy resistance and YY1

Abstract

Conflict of interest

Introduction: Traditional well-established concepts of drug resistance and YY1 signaling

YY1, metabolism, and autophagy

Conclusions

Chapter 15: Yin Yang 1 regulation of tumor cell resistance to chemotherapeutic drugs

Abstract

Conflict of interest

Drug resistance in cancer

Structure and function of the transcription factor Yin Yang 1

YY1 inhibition and its effect on chemoresistance

YY1 and the molecular mechanisms that induce drug resistance

Prognostic significance of YY1 expression in cancer

Concluding remarks

Section IV: YY1 and immunity

Chapter 16: YY1-mediated regulation of type 2 diabetes via insulin

Abstract

Acknowledgments

Conflict of interest

Introduction

Overview: Glucose metabolism

Diabetes mellitus pathology

YY1 and the role of YY1 in T2DM

Discussion

Chapter 17: YY1 expression and PD-1 regulation in CD8 T lymphocytes

Abstract

Conflict of interest

Introduction

Programmed death 1: General characteristics

Expression of PD1 in various tissues and cells

Cell signaling mediated by PD1-PDL1/2 interaction

Regulation of PD1 expression

Regulation and enabling of PD1 expression by various inhibitors

Role of YY1 in the regulation of PD1 expression

Concluding remarks and perspectives

Chapter 18: The role of YY1 in the pathogenesis of rheumatoid arthritis: A tale of cytokines, ncRNAs, and aberrant fibroblast-like synoviocytes (FLSs)

Abstract

Acknowledgments

Conflict of interest

Introduction

Rheumatoid arthritis

YY1

YY1 and RA

Putative pathways

Clinical significance

Conclusions

Index

Copyright

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Aims and Scope

The transcription factor Yin Yang 1 (YY1) exerts pleiotropic activities in the regulation of various gene transcriptions and posttranscriptions in the majority of human cancers. YY1 plays a pivotal role in the regulation of cell viability, cell proliferation, cell signaling pathways, invasion, metastasis, and response to both chemotherapeutic and immunotherapeutic drugs. In addition, YY1 also plays an important role as a prognostic biomarker in many cancers. Noteworthy the inhibition of YY1 DNA-binding activity or its knockdown reversed the aforementioned protumorigenic activities. While the field of YY1 in cancer continues to expand and many recent reviews were reported, although focused in particular areas, however there has not been a published book on YY1 that covers an update and a broad overall information on its multitude of activities and their underlying molecular and genetic mechanisms nor the potential therapeutic interventions targeting YY1.

The main aims of this volume are to cover updated review chapters by experienced investigators that include the following topics: (i) general properties and characterization of YY1; (ii) molecular YY1 transcription and posttranscription; (iii) role of microRNAs and epigenetics in the regulation of YY1 transcription; (iv) molecular mechanisms of YY1 overexpression in human cancers and its prognostic significance; (v) YY1 as an oncogene and its regulation of various tumor suppressor gene products; (vi) role of YY1 in promoting invasion, EMT, and metastasis; (vii) YY1 regulation of the cancer stem cell phenotype; (viii) YY1 regulation of metabolism and autophagy; (ix) YY1 regulation of tumor cell resistance to both chemo- and immunotherapeutic drugs; (x) preclinical antitumor responses by targeting YY1 both in vitro and in vivo; and (xi) future perspectives and the design of new YY1 nontoxic inhibitors for cancer therapy.

Clearly, this book will encompass an overall approach of the current state of art and our understanding of the pleiotropic roles of YY1 in various cancers and future therapeutic applications. This book will serve as a significant reference book for new investigators and established investigators and students.

About the Editor

Dr. Benjamin Bonavida, PhD, editor, is currently Distinguished Research Professor at the University of California, Los Angeles (UCLA). He is affiliated with the Department of Microbiology, Immunology and Molecular Genetics, UCLA David Geffen School of Medicine. His research career, thus far, has focused on investigations in the fields of basic immunochemistry and cancer immunobiology. His research investigations have ranged from the biochemical, molecular, and genetic mechanisms of cell-mediated killing and tumor cell resistance to chemo-immunocytotoxic drugs. The reversal of tumor cell resistance was investigated by the use of various selected sensitizing agents based on molecular mechanisms of resistance. In these investigations, there was the newly characterized dysregulated NF-κB/Snail/YY1/RKIP/PTEN loop in many cancers that was reported to regulate cell survival, proliferation, invasion, metastasis, and resistance. Emphasis was focused on the roles of the tumor suppressor Raf kinase inhibitor protein (RKIP) and the tumor promoter Yin Yang 1 (YY1) and the role of nitric oxide as a chemo-immuno-sensitizing factor. Many of the aforementioned studies are centered on the clinical challenging features of cancer patients’ failure to respond to both conventional and targeted therapies.

The editor has been active in the organization of regular sequential international miniconferences that are highly focused on the roles of YY1, RKIP, and nitric oxide in cancer and their potential therapeutic applications. Several books edited or coedited by the editor have been published. In addition, the editor has been the series editor of books (over 23) published by Springer on Resistance to Anti-Cancer Targeted Therapeutics. In addition, the editor is presently the series editor of three series published by Elsevier/Academic Press on Cancer Sensitizing Agents for Chemotherapy, Sensitizing Agents for Cancer Resistant to Cell Mediated Immunotherapy, and Breaking Tolerance to Anti-Cancer Immunotherapy Lastly the editor is the editor in chief of the Journal Critical Reviews in Oncogenesis. The editor has published over 500 research publications and reviews in various scientific journals of high impact.

Acknowledgments: The editor wishes to acknowledge the excellent editorial assistance of Ms. Inesa Navasardyan who has worked diligently in the completion of this volume, namely, in both the editing and formatting of the various contributions of this volume. Ms. Navasardyan has recently graduated from UCLA (June 2020) and has also contributed a review chapter in this volume on triple negative breast cancer.

The editor acknowledges the Department of Microbiology, Immunology and Molecular Genetics and the UCLA David Geffen School of Medicine for their continuous support. The editor also acknowledges the assistance of Mr. Rafael Teixeira, acquisitions editor for Elsevier/Academic Press, and the excellent assistance of Ms. Samantha Allard, editorial project manager for Elsevier/Academic Press, for their continuous cooperation throughout the development of this book.

Preface

Benjamin Bonavida, Editor

The main aims of this volume are to cover updated review chapters by experienced investigators that include the following topics: (I) general properties and characterization of YY1, (II) expression of YY1 in cancers and prognoses, (III) YY1 and drug resistance, and (IV) YY1 and immunity. In each of these sections, detailed reviews are presented that cover various analyses at the biochemical, molecular, and genetic levels. In addition, many of the reviews strongly suggest the important consideration to target YY1 as a therapeutic, in both cancers and immune responses.

The book contents have been divided into four sections that each deals with a specific aspect of YY1’s involvement.

Section I. General Properties of YY1 in Cancer consists of six chapters.

The chapter by Doctors Małgorzata Figiel and Andrzej Górecki titled The Structure of Yin Yang 1 Protein and Its Importance in the Interaction with Molecular Partners reviews the general properties of YY1 based on the amino acid composition and the various domains and their functions. They describe the four consecutive zinc fingers that interact with DNA, RNA, and proteins and the DNA-binding molecular properties. The complexity of YY1 interaction with various proteins and transcription factors is well discussed, and they present the various structural aspects of YY1 in detail. This chapter provides a good reference.

The chapter by Doctors Silvia Vivarelli, Luca Falzone, and Massimo Libra titled YY1 and Noncoding RNAs: A Two-way Relationship reviews in detail the interrelationship between YY1 and the noncoding RNAs and how their dysregulation plays a critical role in oncology. The authors reviewed the regulation of YY1 by various subtypes of ncRNAs and the role of YY1 in the up- or downregulation of ncRNAs in cancer. They discuss the importance of the two-way communications between YY1 and ncRNAs in the pathogenesis of cancer.

The chapter by Doctors Gustavo Ulises Martinez-Ruiz and Abigail Morales-Sanchez titled YY1 Regulation of the Cancer Stem Cell Phenotype reviews the important cancer stem cell (CSC) subset that exhibit unique properties governing their roles in metastasis, relapses, and resistance to anticancer therapeutics. The authors describe the close relationship between the pleiotropic protumoregenic activities performed by YY1 in cancer and their role in the regulation of the CSC phenotype and their functions.

The chapter by Doctors Eda Acikgoz, Leyla Sati, and Gulperi Oktem titled YY1 Involvement in Embryonic Development and Cancer discusses the close relationship between the development of cancer and its shared molecular and genetic manifestations with embryonic development. Particular attention has focused on the pleiotropic activities of YY1 in cancer and embryonic development. The authors made a good argument in bridging the embryonic development, oncogenesis, and stem cell biology.

The chapter by Doctors Ian Timothy Sembiring Meliala, Rendy Hosea, Vivi Kasim, and Shourong Wu titled Yin and Yang of YY1 Regulation on Tumor Metabolic Reprogramming discusses the role of cancer cells to reprogram the metabolism by altering the catabolism, anabolism, and the redox balance; these are for the cancer cells to accommodate their bioenergetic, biosynthesis, and homeostatic needs. They describe the role of YY1 in the modulation of various signaling pathways involved in the metabolic reprogramming. They suggest that targeting cancer cell metabolism via the inhibition of YY1 may be a strategic approach in the treatment of various cancers.

The chapter by Doctors Yanjun Li, Ian Timothy Sembiring Meliala, Mankun Wei, and Vivi Kasim titled YY1 and Tumor Metastasis Regulation reviews the complex development of metastases and their phenotypic changes and their support by various factors including angiogenesis. They review the prominent role of YY1 in the regulation of many genes that are essential for the metastatic process. These findings suggest the therapeutic potential of targeting YY1 for the prevention and response to conventional therapies.

Section II. Expression of YY1 in Cancers and Prognoses consists of five chapters.

The chapter by Doctors Gabriele Michele, Testa Giuseppe, and Hansen Anders titled Molecular Mechanisms of YY1 Overexpression in Human Cancers and Its Prognostic Significance describes the prognostic significance of YY1 expression in many cancers. They introduce which criteria define prognostic biomarkers. They also examined the alterations of YY1 expression levels in various cancers. They also describe the mutations on YY1 that lead to contrasting effects in the same tumor. They also focused on breast cancer as a model for other cancers. The authors present their perspectives for gaps in YY1 analyses and interpretations and suggest future studies.

The chapter by Inesa Navasardyan and Benjamin Bonavida titled YY1 is Involved in the Pathogenesis and Malignant Properties of Human Triple-Negative Breast Cancer (TNBC) reviews the pathogenesis of the triple negative subset of breast cancer (TNBC) and the mechanisms by which YY1 is implicated. The authors have identified various factors/pathways regulated by YY1 that are responsible for the phenotypic and malignant properties of TNBC. Among these factors, they include the regulation by various miRNAs, the regulation of gene products in the NF-kB/YY1/SNAIL/RKIP/PTEN loop, the YY1/LINCOO152/PTEN axis, the mtp53/PARP1/YY1 axis, the regulation of the Flap endonuclease 1, and the regulation of BRCA. Such findings suggest new therapeutic targets to treat the highly resistant TNBC in patients.

The chapter by Doctors Dominika Kwiatkowska and Adam Reich titled YY1 is a Potential Key Player in the Pathogenesis of Malignant Melanoma reviews the highly malignant human melanoma and the current milestone in the treatment by immunotherapy with significant durable responses in a subset of patients. The authors review the biology of YY1 overexpression in melanoma and the link between the key role of YY1 in several metabolic processes during embryogenesis and development of melanoma. They also discuss the role of YY1 in the transcription of Snail and resulting in the epithelial mesenchymal transition (EMT) and metastasis. In addition, they discuss the role of YY1 autophagy and lysosomal biogenesis in melanoma cells.

The chapter by Doctors Mario Morales-Martinez and Mario I. Vega titled Participation of Different miRNAs in the Regulation of YY1: Their Role in Pathogenesis, Chemoresistance, and Therapeutic Implication in Hematologic Malignancies reviews the role of various miRNAs in the regulation of various functions mediated by YY1 in human hematological malignancies. They review the mechanisms by which miRNAs regulate the role of YY1 in rendering tumor cells resistant to chemotherapeutic drugs. They also discuss the role of YY1 in the pathogenesis of hematological malignancies. They also discuss the therapeutic implications of the findings.

The chapter by Doctors Mengzhen Dong, Yongning Xin, and Likun Zhuang titled Role, Regulatory Mechanism, and Clinical Correlation of YY1 in HCC reviews the highly malignant hepatocellular carcinoma (HCC) and the lack of sensitive and specific diagnostic methods. YY1 is overexpressed in HCC, and it has been reported in HCC to regulate proliferation, metastasis, angiogenesis, metabolic disorder, apoptosis, and drug resistance. In addition, YY1 also regulates the activation of oncogenes and the inhibition of tumor suppressor genes. YY1 also was associated with poor disease-free survival and overall survival.

Section III. YY1 and Drug Resistance consists of four chapters.

The chapter by Doctor Maria Jose Barrero titled Targeting YY1 in Cancer Through Histone Acetylation reviews the notion that transcription factors may be considered as drug targets using strategies of using chemical probes to target epigenetic factors that are required for the transcription factors to stimulate transcription. Such epigenetic-induced drugs interfere with the expression of genes associated with superenhancers (SEs). Noteworthy, YY1 was reported to facilitate enhancer–promoter interactions that play an important role in the maintenance of SEs in cancer cells. Hence the author discusses the therapeutic implications of these findings.

The chapter by Doctor Benjamin Bonavida titled The Role of YY1 in Drug Resistant Cancer: Involvement of the YY1/PTEN/PP2A/H2Ax/Rad51 Axis reviews the various mechanisms that YY1 utilizes to regulate cancer cells resistant to cytotoxic drugs. A new mechanism of resistance was recently reported in which YY1 is involved in the regulation of DNA damage by cytotoxic drugs and the inhibition of phospho-PTEN translocation into the nucleus and activation of DNA repair genes, H2AX and Rad51. A loop has been constructed consisting of YY1, PTEN, PP2A, H2AX, and Rad51 gene products that altogether regulate the resistance to cytotoxic drugs by inhibiting DNA repair. This new loop offers a rationale for targeting YY1 to reverse drug resistance.

The chapter by Doctor Paul Dent titled Chemotherapy Resistance and YY1 reviews the literature on the various mechanisms by which cancer cells adapt to preserve their survival upon exposure to chemotherapeutic drugs, for example, the upregulation of antiapoptotic gene products and the inhibition of proapoptotic gene products, and the interaction of YY1 with histone deacetylases resulting in transcriptional repression. In this review, Doctor Dent integrates the role of YY1 into the various complex mechanisms of resistance.

The chapter by Doctors Tania V. Lopez-Perez, Belen Tirado-Rodriguez Mario Morales-Martinez, Mayra Montecillo-Aguado, and Sara Huerta-Yepez titled Yin Yang 1 Regulation of Tumor Cell Resistance to Chemotherapeutic Drugs reviews investigations reported by themselves and others on the various molecular mechanisms by which YY1 regulates tumor cell resistance to various chemo- and immunotherapeutic drugs. They use various examples of various tumors, in vitro and in vivo, to underlie various gene products regulated by YY1 and responsible for resistance. They suggest the potential therapeutic application of inhibitors for YY1 to reverse resistance.

Section IV. YY1 and Immunity consists of three chapters.

The chapter by Feodora Roxanne Kosasih and Doctor Benjamin Bonavida titled YY1-Mediated Regulation of Type 2 Diabetes via Insulin reviews the various signaling pathways involved in the pathogenesis of diabetes mellitus type 2 (T2DM) and whether YY1 is also implicated in cross talks with these signaling pathways, hence demonstrating the involvement of YY1 in the regulation of T2DM. The analyses revealed that, indeed, YY1 is involved in various aspects in the regulation of T2DM, and there we suggested that it be considered as a therapeutic target.

The chapter by Roni Touboul and Doctor Benjamin Bonavida titled YY1 Expression and PD-1 Regulation in CD8 T Lymphocytes reviews the role of YY1 in the regulation of the checkpoint inhibitory receptor on the antitumor CD8CTLs and therefore plays a role in the inactivation of these effector cells and contributes in failure of the immune response to eradicate the tumor. The analyses revealed that, indeed, YY1 regulates positively the expression of PD1 on CD8 + CTLs, both transcriptionally and indirectly through cross talk signaling pathways. Since YY1 has been reported to exert various protumoregenic activities, these authors stipulated that targeting YY1 will have a dual effect on both the CD*+CTLs and on the tumor cells. This dual effect will amplify the antitumor response by the use of YY1 inhibitors.

The chapter by Yuhao Wang and Doctor Benjamin Bonavida titled The Role of YY1 in the Pathogenesis of Rheumatoid Arthritis: A Tale of Cytokines, ncRNAs, and Aberrant Fibroblast-like Synoviocytes (FLSs) reviews the interrelationship between the onset of rheumatoid arthritis (RA) and YY1. Several reported studies have described interactions between YY1 and various pathways that are involved in the amplification of cytokines in the peripheral blood mononuclear cells that enhance the activity of the RA-associated fibroblast-like synoviocytes (RAFLs). Through the analysis, we revealed two putative pathways that link YY1 and RA, namely, the TNF-α/NF-κB/YY1/ANRIL/miR-122-5p axis and the TNF-α/Notch1/YY1/c-myc axis. Accordingly, we proposed to add YY1 as a potential therapeutic target for both the prevention and treatment of T2DM.

Overall, this book covers the current state of art and our understanding of the pleiotropic roles mediated by YY1 in various cancers and the immune response and future therapeutic applications. This book will serve as a significant reference for new investigators, students, established investigators, and pharmaceutical and biotech enterprises.

Contributors

Eda Acikgoz     Department of Histology and Embryology, Faculty of Medicine, Van Yuzuncu Yil University, Van, Turkey

Hansen Anders     Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States

Maria Jose Barrero     Center for Regeneration Medicine in Barcelona (CMRB), Avinguda de la Granvia de l‘Hospitalet, Barcelona, Spain

Benjamin Bonavida     Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, United States

Paul Dent     Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, VA, United States

Mengzhen Dong

Institute of Hepatology

Department of Infectious Disease, Qingdao Municipal Hospital, Qingdao University

Digestive Disease Key Laboratory of Qingdao, Qingdao, China

Luca Falzone     Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy

Małgorzata Figiel     Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland

Testa Giuseppe

Department of Experimental Oncology, IEO, European Institute of Oncology, IRCCS

Department of Oncology and Hemato-Oncology, University of Milan

Human Technopole, Milan, Italy

Andrzej Górecki     Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland

Rendy Hosea

The Key Laboratory of Biorheological Science and Technology, Ministry of Education

The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing, China

Sara Huerta-Yepez     Oncological Diseases Research Unit, Children's Hospital of Mexico Federico Gomez, Mexico City, Mexico

Vivi Kasim

The Key Laboratory of Biorheological Science and Technology, Ministry of Education

The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University

State and Local Joint Engineering Laboratory for Vascular Implants, Chongqing, China

Feodora Roxanne Kosasih     Department of Psychology, University of California Los Angeles, Los Angeles, CA, United States

Dominika Kwiatkowska     Department of Dermatology, Institute of Medical Sciences, Medical College of Rzeszow University, Rzeszów, Poland

Yanjun Li

The Key Laboratory of Biorheological Science and Technology, Ministry of Education

The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing, China

Massimo Libra

Department of Biomedical and Biotechnological Sciences

Research Center for Prevention, Diagnosis and Treatment of Cancer, University of Catania, Catania, Italy

Tania V. Lopez-Perez

Oncological Diseases Research Unit

CONACYT-Oncological Diseases Research Unit, Children's Hospital of Mexico Federico Gomez, Mexico City, Mexico

Gustavo Ulises Martinez-Ruiz

Research Division, School of Medicine, National Autonomous University of Mexico

Children's Hospital of Mexico Federico Gomez, Mexico City, Mexico

Ian Timothy Sembiring Meliala

The Key Laboratory of Biorheological Science and Technology, Ministry of Education

The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing, China

Gabriele Michele

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States

Department of Experimental Oncology, IEO, European Institute of Oncology, IRCCS, Milan, Italy

Mayra Montecillo-Aguado     Oncological Diseases Research Unit, Children's Hospital of Mexico Federico Gomez, Mexico City, Mexico

Mario Morales-Martinez

Molecular Signal Pathway in Cancer Laboratory, UIMEO, Oncology Hospital, Siglo XXI National Medical Center, IMSS

Postgraduate Unit, Faculty of Medicine, National Autonomous University of Mexico, Mexico City, Mexico

Abigail Morales-Sanchez     Research Division, School of Medicine, National Autonomous University of Mexico, Mexico City, Mexico

Inesa Navasardyan     Department of Biophysics, School of Physical Sciences, University of California Los Angeles, Los Angeles, CA, United States

Gulperi Oktem

Department of Histology and Embryology, Faculty of Medicine

Department of Stem Cell, Institute of Health Science, Ege University, Izmir, Turkey

Adam Reich     Department of Dermatology, Institute of Medical Sciences, Medical College of Rzeszow University, Rzeszów, Poland

Leyla Sati     Department of Histology and Embryology, Faculty of Medicine, Akdeniz University, Antalya, Turkey

Belen Tirado-Rodriguez     Oncological Diseases Research Unit, Children's Hospital of Mexico Federico Gomez, Mexico City, Mexico

Roni Touboul     Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, United States

Mario I. Vega

Molecular Signal Pathway in Cancer Laboratory, UIMEO, Oncology Hospital, Siglo XXI National Medical Center, IMSS, Mexico City, Mexico

Department of Medicine, Hematology-Oncology Division, Greater Los Angeles VA Healthcare Center, UCLA Medical Center, Jonsson Comprehensive Cancer Center, Los Angeles, CA, United States

Silvia Vivarelli     Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy

Yuhao Wang     Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, United States

Mankun Wei

The Key Laboratory of Biorheological Science and Technology, Ministry of Education

The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing, China

Shourong Wu

The Key Laboratory of Biorheological Science and Technology, Ministry of Education

The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University

State and Local Joint Engineering Laboratory for Vascular Implants, Chongqing, China

Yongning Xin

Institute of Hepatology

Department of Infectious Disease, Qingdao Municipal Hospital, Qingdao University

Digestive Disease Key Laboratory of Qingdao, Qingdao, China

Likun Zhuang

Institute of Hepatology

Department of Infectious Disease, Qingdao Municipal Hospital, Qingdao University

Digestive Disease Key Laboratory of Qingdao, Qingdao, China

Section I

General properties of YY1 in cancer

Chapter 1: The structure of Yin Yang 1 protein and its importance in the interaction with molecular partners

Małgorzata Figiel; Andrzej Górecki    Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland

Abstract

Yin Yang 1 (YY1), a multifunction protein pivotal to numerous cellular processes, is one of the most evolutionarily preserved eukaryotic proteins, suggesting a perfect functional selection. Another unusual feature of YY1 is its amino acid composition, with several low-complexity regions enriched in D/E, H, and GA/GK residues. All of them map to the disordered N-terminal fragment of YY1. Its C-terminus contains four consecutive zinc fingers, which were shown to interact with DNA, RNA, and proteins. Binding to DNA has been studied in greatest detail. Binding to RNA is less understood, although YY1 certainly exploits different mechanisms and interactions. YY1 is also engaged in a plethora of protein-protein interactions, in which it functions as a cofactor, regulator, and molecular switch, controlled by binding partners, posttranscriptional modifications, and subcellular translocations. A thorough insight into the structural aspects of various YY1 interactions allows for a better understanding of the biological processes in which YY1 participates. This chapter is devoted to the structural aspects of the YY1, which have direct consequences in its interaction with molecular partners.

Keywords

Yin Yang 1 (YY1); Structure; DNA-protein interaction; RNA-protein interaction; Protein-protein interaction; Transcription regulation; Carcinogenesis

Abbreviations

AAV 

adeno-associated virus

DBD 

DNA-binding domain

IDP 

intrinsically disordered protein

NTF 

N-terminal fragment

REPO 

recruitment of polycomb

YY1 

Yin Yang 1

ZF 

zinc finger

Conflict of interest

No potential conflicts of interest were disclosed.

Evolutionary conservation of Yin Yang 1

Since some of the published research consider Yin Yang 1 (YY1) proteins present in nonhuman organisms, it seems necessary to compare first their structures to facilitate the assessment of the obtained results with the human protein. YY1 is found in all vertebrates, and its orthologs can also be found in other phylogenetically distant animals, such as fruit fly (PHO protein) [1] and sea urchin [2]. The function of the human YY1 protein is certainly particularly intensively studied, although research is also carried out for mouse [3, 4], rat [5, 6], fruit fly [7, 8], cattle [9, 10], hamster [11, 12], chicken [13, 14], frog [15, 16], rabbit [17, 18], pig [19, 20], dog [21, 22], sheep [23, 24], goat [25, 26], horse [27], zebrafish [28, 29], or the aforementioned sea urchin [2, 30]. Fig. 1 shows the alignment of the listed orthologs.

Fig. 1 Global alignment of YY1 studied orthologs. Sixteen sequences were used with the following designations, species, and access codes: HsYY1, human ( Homo sapiens ), P25490; MmYY1, mouse ( Mus musculus ), Q00899; RnYY1, rat ( Rattus norvegicus ), NP_775412.1; PHO, fruit fly ( Drosophila melanogaster ), Q8ST83; BtYY1, cattle ( Bos taurus ), A5D7T6; MaYY1, hamster ( Mesocricetus auratus ), A0A1U8BW63; GgYY1, chicken ( Gallus gallus ), NP_001026381.1; XlYY1, clawed frog ( Xenopus laevis ) , Q6DDI1; SsYY1, pig ( Sus scrofa ), K9IVK7; ClYY1, dog ( Canis lupus familiaris ), E2RHE9; OaYY1, sheep ( Ovis aries ), XP_0278.1; ChYY1, goat ( Capra hircus ) A0A452EH31; MmuYY1, macaque ( Macaca mulatta ), H9YYS6; EcYY1, horse ( Equus caballus ), XP_023484159.1; DrYY1, zebrafish ( Danio rerio ), Q7T1S; SpYY1, purple sea urchin ( Strongylocentrotus purpuratus ), W4Y3K9. Human YY1 sequence is set as a reference. Each amino acid type is represented by a different background color, so a vertical line with the same color indicates the conservation among all the sequences. Additional dark blue vertical lines indicate hidden insertions. Residue conservation and consensus indications are shown below the sequences together with the regions designated for HsYY1. ClustalW was used for alignment ( https://www.ebi.ac.uk/Tools/msa/clustalo/ ), Jalview software for visualization [31].

All the studied orthologs show high sequence conservation, especially within the four zinc fingers (ZFs) forming the DNA-binding domain (DBD). Only two most phylogenetically distant orthologs showed variability of single amino acid residues. This makes DBD one of the most evolutionarily conserved domains of all transcription factors [32]. It is identical in all vertebrates except for one or two species-specific amino acid changes. YY1 has maintained its DBD without any amino acid changes in the last 600 million years, which is one of the most extreme cases of evolutionary preservation of a eukaryotic gene, suggesting a perfect functional selection [1]. It is worth noting that the conservation includes not only the residues directly involved in the interaction with DNA (see in the succeeding text) but also all the other DBD-forming residues.

The remaining part of the YY1, referred to as the N-terminal fragment (NTF), is less evolutionarily conserved. In this fragment the conservation concerns mainly vertebrates and is much lower for PHO and SpYY1 than for the other homologs. Still the conservation is high enough that HsYY1 may substitute the function of PHO protein [33]. Among the vertebrates the differences are primarily small deletions or insertions in the regions of low complexity of the amino acid composition.

Structure of human YY1

The human YY1 gene is located on chromosome 14 [34] and encodes pre-mRNA consisting of five exons. Only one isoform of YY1 is common, formed by 414 amino acid residues, but three or seven additional shorter isoforms of unknown functions were also postulated [1, 35]. YY1 is ubiquitously expressed, and its level of expression is similar in all tissues [36].

Based on the primary structure of the protein, six fragments are distinguished [36]: Acidic 1 (aa 1–54), His-cluster (aa 55–80), Acidic 2 (aa 81–154), GA/GK Rich (aa 155–198), Spacer (aa 199–295), and DBD (296–414) (also referred to as ΔYY1 [37]). The first five fragments (aa 1–295) together constitute the NTF [38]. They partly overlap with the evolutionarily preserved regions (Fig. 1). The His-cluster, containing an unusual stretch of 11 histidine residues, is somewhat less conserved. In other organisms, this string has a different length or does not occur at all. In addition to DBD, two short fragments of the linker region are most conserved, referred to as Domain 1 and Domain 2 (formed by amino acid residues 203–226 and 250–281, respectively). Interestingly, these domains also occur among the YY1 protein paralogs, which include the YY2 and REX1 proteins [1]. In the literature, Domain 1 is also called the recruitment of polycomb domain (REPO) [39] or oncoprotein-binding domain (OPB) [40].

The spatial structure of YY1 was resolved with atomic resolution only for its two fragments. In both cases, these are cocrystalline structures obtained in the presence of molecular partners: nucleic acid or protein.

The first resolved structure was the structure of DBD in a complex with a 20-nucleotide dsDNA encoding a fragment of the adeno-associated virus (AAV) P5 initiator (PDB: 1udb). In this case, YY1 fragment of aa 293–414 was crystallized, and a slightly shorter fragment was solved (aa 295–408) [37]. The spatial structure shows four ZFs of C2H2 type located in the DNA major groove (Fig. 2). A more detailed description will be presented in the next section (Fig. 3).

Fig. 2 Spatial structure of YY1 fragments interacting with molecular partners. The REPO domain (resolved fragments include aa 206–214 and 219–225) binding to MBTD1 protein (PDB: 4C5I) [8]. The DBD (resolved fragments aa 295–408) binding to dsDNA of AAV P5 initiator sequence (PDB: 1UBD) [37]. Orange, red, yellow, green, and blue colors denote REPO domain, and ZFs from the first to the fourth, respectively. Accelrys DS Visualizer v2.0.1 was used for visualization.

Fig. 3 Detailed representation of the YY1-DNA interaction scheme. Bold boxes represent the canonical interaction of ZFs with the DNA strands (coding and template strand are represented by the upper and bottom box, respectively). Capital letters indicate the interaction with nucleobases of the given strand and position. Green color represents direct interaction, blue color —interaction mediated by a water molecule. The names of amino acid residues and nucleobases involved in the interaction are bold. The sequence of AAV P5 initiator and the sequence logo of YY1 consensus sequence [22] are presented above the scheme. To the right of the interaction schemes, spatial structures are presented of the complexes formed by individual ZFs. Smaller embeddedness of the ZF1 is embedded in the DNA major groove to a smaller extent than the other ZFs that is clearly seen. Accelrys DS Visualizer v2.0.1 was used for visualization of the 1UBD structure.

The second resolved structure included the REPO domain with a fragment of the MBTD1 protein (Q05BQ5, aa 130–566) (PDB: 4C5I) [8]. In this case the crystalized YY1 fragment covered aa 199–228, while two shorter fragments were solved (aa 206–214 and 219–225), forming the structure of an antiparallel β sheet located inside the hydrophobic pocket of the MBTD1 protein (Fig. 2). Three more structures were solved for an analogous complex from the fruit fly (PDB: 4C5E, 4C5G, and 4C5H). Slightly longer fragments of the PHO protein (aa 141–172 or 116–246) were cocrystallized with the corresponding fragment of the SFMBT protein (aa 531–980)—fruit fly homolog of MBTD1 [8]. The solved fragment of the PHO protein (aa 141–172) corresponds to HsYY1 aa 202–226. The obtained structure is analogical, formed by two antiparallel β strands connected by a short β harpin. The interaction interface of this PHO fragment with the partner is also identical.

The remaining part of YY1 is considered as an intrinsically disordered region. This was proved based on both bioinformatic analysis of the protein sequence and numerous physicochemical experiments carried out for the full length YY1 and its NTF. Features that indicate disorder include increased proteolytic susceptibility, anomalous migration during SDS-PAGE separation (YY1 with a molar mass of 44.7 kDa and NTF with a molar mass of 32.2 kDa have apparent masses of 55 and 43 kDa, respectively), hydrodynamic radius of gyration increased to a value characteristic for a premolten globule, circular dichroism spectrum characteristic for intrinsically disordered proteins (IDPs), and tryptophan fluorescence emission spectrum indicating high solvent exposure. Nevertheless, denaturing analysis showed that NTF retains a residual content of secondary structure and the potential for further structurization. Thus under appropriate conditions (e.g., upon interaction with molecular partners) NTF can reversibly adopt an ordered secondary structure (β sheet structure is expected). Interestingly and consistently with this conclusion, the distinct features of disorder are manifested by sole NTF rather than the full-length YY1. Probably the intramolecular interaction between NTF and DBD leads to partial ordering of the former [38].

It is worth to add that a similar analysis was performed for the YY2 protein—YY1’s retroposon [1]. While its DBD behaves analogously to DBD of YY1, its NTF shows less momentous properties of an IDP [41].

Interaction with DNA

The C-terminal part of YY1 consists of four ZFs. Each of them is formed by about 30 amino acid residues congruent with the classic structure consisting of two short, 3-aa β sheets and an 11-aa α helix. Such a small structure can form a structural domain due to the binding of a single zinc ion, which efficiently stabilizes the domain’s conformation. The zinc ion is chelated by two cysteine residues, located within the first β sheet and β turn, and by two histidine residues located at positions 7 and 11 of the α helix. ZFs are connected by short linkers: two amino acid long between ZF1 and ZF2 and three amino acid long between the remaining ones. ZFs are best known as domains specifically binding dsDNA, that is, recognizing a particular nucleotide sequence. Nevertheless, their interactions with ssDNA, ssRNA, and proteins are now considered much more common than previously thought [42], although the name of this YY1 part refers to the interaction with dsDNA. The only known spatial structure of this fragment was resolved with atomic resolution due to cocrystallization of this domain with DNA (Fig. 2). The interaction between YY1 and DNA has two components: nonspecific, in which amino acid residues participate mainly in interaction with the DNA phosphate backbone, and specific, where amino acid residues interact directly with the nucleobases. The latter is possible only inside the DNA major groove [43]. Figs. 3 and 5 show the details of the interaction specificity determined for DBD and the AAV P5 initiator. The canonical amino acid residues located at positions 2, − 1, 3, and 6 of the α-helix are responsible for the specific interaction of each ZF and DNA. These residues in this order recognize subsequent DNA base pairs, with the amino acid residue at position 2 recognizing the nucleobase of the other strand than the remaining three residues [43]. The specific sequence recognition by YY1 has been determined by a variety of techniques, and the most common consensus sequence is GCCATnTT [45]. When the sequence is presented with the indication of the significance of particular nucleotides, for example, in the form of a sequence logo, it is often slightly wider and includes 12 nucleotides (Fig. 3). However, most of the interactions concern nine nucleotides and ZFs 2–4 [37]. The significance of the first ZF may be limited due to the shorter linker between the first and second ZFs, which introduces steric restrictions on the optimal location of adjacent ZFs in the major groove [46]. Recently, Chen et al. employed cysteine mutagenesis approach to selectively impair particular ZFs of YY1. Their analysis confirmed that ZFs 1 and 4 contribute little to DNA-binding and transcriptional activity of YY1 [40].

Fig. 4 Significance of the mutation T372R that correlates with sporadic insulinomas. The T372 residue side chain (red) is too short for direct interaction with the nucleobase (left panel), preventing a specific interaction at position 10 for the WT protein. Substitution T372R changes the recognized sequence, enabling interaction in this position with cytidine and 5′-shifting the recognized sequence toward 1ZF. Accelrys DS Visualizer v2.0.1 was used for visualization of the 1UBD structure. Sequence logos were prepared based on [6].

Fig. 5 Comparison of the DBD binding to DNA (upper panel) and RNA (bottom panel). Letters in frames denote residues with positions either resolved using X-ray crystallography (for DBD-DNA interaction [37]) or assigned from 3-D triple-resonance, 3-D NMR spectra (for DBB-RNA interaction [44]). In case of DBD-DNA interaction with 20 nt dsDNA AAV initiator sequence (5′-AGGGTCTCCATTTTGAAGCG-3′) is referred. Green, blue, and yellow colors indicate the following types of interaction: direct, mediated through water, and both types, respectively, while square and rectangle indicate specific and unspecific interaction. In case of DBD-RNA, bold letters in red background indicate the residues for which ¹⁵N-HSQC spectra were significantly perturbed during the interaction with 14 nt ssRNA semi-specific sequence (5’- AGGCGAUGGUGAGC-3’). For comparison, grey rectangles represent contacts with DNA.

The interaction of YY1 with DNA is relatively weak compared with what would be expected for such a long recognition sequence [47]. The dissociation constant of this interaction ranges from 0.2 μM (IgH enhancer lE1) to 12 μM (SRE c-fos promoter). The value indicates relatively low specificity of the interaction, since the affinity to a random dsDNA sequence is about 50 μM and thus only slightly lower than the affinity to the cognate elements [48]. The kinetic measurements indicate that for DBD binding to specific DNA sequence, the association constant (kon) is in the range of 1–3 × 10⁶ M− 1 s− 1, while the dissociation constant (koff) is about 0.1–0.3 s− 1[48]. Therefore the low specificity is primarily due to the high koff value, since for many other nucleoproteins this value is much lower [49, 50]. The low specificity is highly unexpected, since specific recognition is crucial for the proper functioning of transcription factors. Therefore it is believed that in vivo the YY1-DNA binding is supported by additional interactions with other proteins. Such interactions would decrease the koff value, thus increasing the binding affinity and making it more specific. The presence of tandem YY1 sites in a DNA region increases its affinity for YY1. However, the nature of this process has not yet been clarified [45].

During the interaction of ZFs with DNA, the arrangement of the recognizing helix is fixed in relation to the major groove. Its N-terminus is located closer to the nucleotides than the C-terminus. This causes the amino acid residues at the C-terminus to have longer side chains than those located at its N-terminus. The nonoptimal side chain of T273 residue in position 6 of ZF3 helix is unable to interact with the nucleobase, which explains the occurrence of no specificity defined as n in the recognized GCCATnTT sequence.

T372R substitution in ZF3 was frequently observed, correlating with the occurrence of nonhereditary insulinoma. The arginine residue introduced at this site is better suited for specific interaction with DNA, both because of its size and its chemical nature. Therefore a change of the sequence preferentially recognized by this mutant was not surprising. However, the recognized sequence unexpectedly shifted toward the 5′ end, indicating a greater role of the unmodified first ZF, which in the wild-type protein interacts with DNA only through K315 [6] (Fig. 4). These observations imply the complexity of the DNA-YY1 interaction process, where modular description of the recognition is not sufficient to explain the observed findings. The linker connecting the first and second ZF is also postulated to play a role in this process. Its length, shorter than typical, may hinder the optimal, simultaneous steric fit of all four ZFs to DNA. The introduced mutation, causing an indirect decrease in the fourth ZF interaction with DNA, would allow for more accurate adjustment of the first finger [46].

The analysis of the secondary structure content of the T372R DBD and YY1 mutants, based on measurements of circular dichroism, showed that the proteins carrying the mutations have secondary structure indistinguishable from the wild types. The presence of a positively charged amino acid residue in a site predestined for interaction with DNA should result in increased affinity. This is indeed the case for two out of four studied sequences, for which the affinity increases several times upon introducing the mutation. The interaction with the other two promoter sequences is weakened. Bearing in mind the specific nature of the interaction of the residue located in the position 372 with DNA, the obtained results become understandable [46].

In addition, experiments on full-length proteins and their variants truncated to the DBD allowed to determine the importance of the NTF of YY1 for this process. NTF does not directly participate in the interaction with DNA, but it turns out to affect the interaction parameters. The obtained results lead to the conclusion that the NTF affects the affinity of YY1 to DNA in a significantly sequence-dependent manner.

Interaction with RNA

Apart from the well-established interaction with DNA, YY1 was also shown to bind to RNA [16, 44, 51–53]. However, little structural and functional details of YY1-RNA binding have been elucidated so far. Opposing reports describe it to engage different parts of YY1: either its DBD [44, 51] or