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Cancers
Special Issues
Cancer Genetics and Epigenetics: Their Roles and Clinical Implications
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Cancer Genetics and Epigenetics: Their Roles and Clinical Implications

A special issue of Cancers (ISSN 2072-6694). This special issue belongs to the section "Molecular Cancer Biology".

Deadline for manuscript submissions: 15 September 2025 | Viewed by 14694

Special Issue Editors

Prof. Dr. Armita Bahrami

E-Mail Website
Guest Editor
Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30307, USA
Interests: genetics of sarcoma; pathology of sarcoma; pathology of pediatric solid tumors; pathology of bone and soft tissue tumors; genetics of pediatric solid tumors; pathology and genetics of pediatric melanoma; telomerase and cancer
Dr. Ying Qing

E-Mail Website
Guest Editor
Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
Interests: epigenetics in cancer; epitranscriptomics in cancer; DNA modification regulation; RNA modification regulation; gene expression regulation during tumorigenesis; cancer metabolism; obesity and cancer; cancer immunology

Special Issue Information

Dear Colleagues,

Tumor cells undergo critical genetic and epigenetic changes in cancer development and progression. Genetic mutations and alterations in the DNA sequence of specific genes can contribute to the development of cancer by disrupting normal cellular functions. Meanwhile, epigenetic (and epitranscriptomic) modifications such as DNA methylation, histone modifications, and RNA methylation can also affect cancer development by altering gene expression without changing the DNA sequence. Understanding the distinct roles of genetics and epigenetics in cancer is critical for developing targeted and effective therapies. Moreover, it has been recently reported that certain genetic changes (e.g., IDH mutations) could lead to dysregulation of epigenetic signaling to facilitate tumorigenesis. The intersection of cancer genetics and epigenetics has emerged as a dynamic field in cancer research with critical implications for clinical practice.

 This Special Issue aims to focus on the genetics and epigenetics of cancer and their clinical implications for cancer diagnosis and treatment and highlight recent advances in understanding the molecular mechanisms underlying the interplay between cancer genetics and epigenetics. Original research articles, reviews, and perspectives covering a broad range of topics, from the identification of novel oncogenic drivers and epigenetic modifiers to the development of innovative diagnostic and therapeutic strategies, are welcome. We look forward to receiving your contributions.

Prof. Dr. Armita Bahrami
Dr. Ying Qing
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Cancers is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2900 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • cancer genetics
  • cancer epigenetics
  • carcinogenesis
  • cancer prognosis
  • cancer therapeutics
  • genetic mutations
  • DNA methylation
  • histone modifications
  • RNA methylation

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Published Papers (5 papers)

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Research

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12 pages, 2560 KiB  
Article
Acinic Cell Carcinoma in the 21st Century: A Population-Based Study from the SEER Database and Review of Recent Molecular Genetic Advances
by Jaffar Khan, Asad Ullah, Mya Goodbee, Kue Tylor Lee, Abdul Qahar Khan Yasinzai, James S. Lewis, Jr. and Hector Mesa
Cancers 2023, 15(13), 3373; https://doi.org/10.3390/cancers15133373 - 27 Jun 2023
Cited by 2 | Viewed by 2457
Abstract
Background: Acinic cell carcinoma (AciCC) comprises 6–7% of all salivary gland neoplasms and is the second most common salivary gland malignancy in children. Like many salivary gland carcinomas, it is considered low grade but occasionally it behaves aggressively. Understanding the risk factors associated [...] Read more.
Background: Acinic cell carcinoma (AciCC) comprises 6–7% of all salivary gland neoplasms and is the second most common salivary gland malignancy in children. Like many salivary gland carcinomas, it is considered low grade but occasionally it behaves aggressively. Understanding the risk factors associated with recurrence, metastasis, and death is important to determine the counseling and management of individual patients. Older population-based studies are presumed to have been confounded by the misclassification of other neoplasms as AciCC, in particular secretory carcinoma and cystadenocarcinoma. Since diagnostic tools to reliably separate these entities have been available for over a decade, reevaluation of epidemiologic data limited to the 21st century should allow a better characterization of the clinicopathological characteristics of AciCC. Methods: Our study extracted data from the Surveillance, Epidemiology, and End Results (SEER) database for the period 2000 to 2018. Cox regression model analysis was performed to identify risk factors independently affecting survival. Results: Data for 2226 patients with AciCC were extracted from the database. Most patients were females: 59%, and white: 80.5%, with a mean age at diagnosis of 51.2 (SD ± 18.7) years. Most cases (81%) were localized at presentation. Tumor size was less than 2 cm in 42%, 2–4 cm in 47%, and >4 cm in 11%. Low-grade tumors had 5-year survival > 90%, whereas high-grade tumors had survival < 50%. Of the patients with known lymph node status only 7.3% had nodal metastases. Distant metastases were documented in 1.1%, involving lungs 44%, bone 40%, liver 12%, and brain 4%. The most common treatment modality was surgery alone: 63.6% followed by surgery and adjuvant radiation: 33%. A few received chemotherapy (1.8%) or multimodality therapy (1.2%). The 5-year overall survival rate was 90.6% (95%CI 89.1–91.9), and disease-specific survival was 94.6% (95%CI 93.3–95.6). Multivariable cox regression analysis showed that undifferentiated (HR = 8.3) and poorly differentiated tumor grade (HR = 6.4), and metastasis (HR = 5.3) were the worst independent prognostic factors. Other poor risk factors included age > 50 (HR = 3.5) and tumor size > 4 cm (HR = 2.5). Conclusions: In the US, AciCC is more common in middle age white females, and most tumors are less than 4 cm and localized at diagnosis. The most relevant negative prognostic factor was high tumor grade which was associated with higher hazard ratios for death than all other variables, including regional or distant metastases at presentation. Full article
(This article belongs to the Special Issue Cancer Genetics and Epigenetics: Their Roles and Clinical Implications)
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Review

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22 pages, 364 KiB  
Review
Biological Markers of Myeloproliferative Neoplasms in Children, Adolescents and Young Adults
by Aleksandra Ozygała, Joanna Rokosz-Mierzwa, Paulina Widz, Paulina Skowera, Mateusz Wiliński, Borys Styka and Monika Lejman
Cancers 2024, 16(23), 4114; https://doi.org/10.3390/cancers16234114 - 8 Dec 2024
Viewed by 1679
Abstract
Myeloproliferative neoplasms (MPNs) are clonal hematopoietic cancers characterized by hyperproliferation of the myeloid lineages. These clonal marrow disorders are extremely rare in pediatric patients. MPN is reported to occur 100 times more frequently in adults, and thus research is primarily focused on this [...] Read more.
Myeloproliferative neoplasms (MPNs) are clonal hematopoietic cancers characterized by hyperproliferation of the myeloid lineages. These clonal marrow disorders are extremely rare in pediatric patients. MPN is reported to occur 100 times more frequently in adults, and thus research is primarily focused on this patient group. At present, modern diagnostic techniques, primarily genetic, facilitate the identification of the biology of these diseases. The key genes are JAK2, MPL, and CALR, namely, driver mutations, which are present in approximately 90% of patients with suspected MPN. Moreover, there are more than 20 other mutations that affect the development of these hematological malignancies, as evidenced by a review of the literature. The pathogenic mechanism of MPNs is characterized by the dysregulation of the JAK/STAT signaling pathway (JAK2, MPL, CALR), DNA methylation (TET2, DNMT3A, IDH1/2), chromatin structure (ASXL1, EZH2), and splicing (SF3B1, U2AF2, SRSF2). Although rare, myeloproliferative neoplasms can involve young patients and pose unique challenges for clinicians in diagnosis and therapy. The paper aims to review the biological markers of MPNs in pediatric populations—a particular group of patients that has been poorly studied due to the low frequency of MPN diagnosis. Full article
(This article belongs to the Special Issue Cancer Genetics and Epigenetics: Their Roles and Clinical Implications)
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12 pages, 737 KiB  
Review
WNT and TGF-Beta Pathway Alterations in Early-Onset Colorectal Cancer Among Hispanic/Latino Populations
by Cecilia Monge, Brigette Waldrup, Francisco G. Carranza and Enrique Velazquez-Villarreal
Cancers 2024, 16(23), 3903; https://doi.org/10.3390/cancers16233903 - 21 Nov 2024
Cited by 3 | Viewed by 1545
Abstract
Background/Objectives: One of the fastest-growing minority groups in the U.S. is the Hispanic/Latino population. Recent studies have shown how this population is being disproportionately affected by early-onset colorectal cancer (CRC). Compared to corresponding non-Hispanic White (NHW) patients, Hispanic/Latino patients have both higher incidence [...] Read more.
Background/Objectives: One of the fastest-growing minority groups in the U.S. is the Hispanic/Latino population. Recent studies have shown how this population is being disproportionately affected by early-onset colorectal cancer (CRC). Compared to corresponding non-Hispanic White (NHW) patients, Hispanic/Latino patients have both higher incidence of disease and rates of mortality. Two well-established drivers of early-onset CRC in the general population are alterations in the WNT and TGF-Beta signaling pathways; however, the specific roles of these pathways in Hispanics/Latinos are poorly understood. Methods: Here, we assessed CRC mutations in the WNT and TGF-Beta pathways by conducting a bioinformatics analysis using cBioPortal. Cases of CRC were stratified both by age and ethnicity: (1) early-onset was defined as <50 years vs. late-onset as ≥50 years; (2) we compared early-onset in Hispanics/Latinos to early-onset in NHWs. Results: No significant differences were evident when we compared early-onset and late-onset CRC cases within the Hispanic/Latino cohort. These results are consistent with findings from large cohorts that do not specify ethnicity. However, we found significant differences when we compared early-onset CRC in Hispanic/Latino patients to early-onset CRC in NHW patients: specifically, alterations in the gene bone morphogenetic protein-7 (BMP7) were more frequent in early-onset CRC for the Hispanic/Latino patients. In addition to these findings, we observed that both NHW patients and Hispanic/Latino patients with early-onset disease had better clinical outcomes when there was evidence of WNT pathway alterations. Conversely, the absence of TGF-Beta pathway alterations was uniquely associated with improved outcomes exclusively in early-onset Hispanic/Latino patients. Conclusions: In toto, these findings underscore how the WNT and TGF-Beta pathways may act differently in different ethnic groups with early-onset CRC. These findings may set a stage for developing new therapies tailored for reducing cancer health disparities. Full article
(This article belongs to the Special Issue Cancer Genetics and Epigenetics: Their Roles and Clinical Implications)
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22 pages, 8066 KiB  
Review
A–Z of Epigenetic Readers: Targeting Alternative Splicing and Histone Modification Variants in Cancer
by Nivedhitha Mohan, Roderick H. Dashwood and Praveen Rajendran
Cancers 2024, 16(6), 1104; https://doi.org/10.3390/cancers16061104 - 9 Mar 2024
Cited by 3 | Viewed by 2664
Abstract
Epigenetic ‘reader’ proteins, which have evolved to interact with specific chromatin modifications, play pivotal roles in gene regulation. There is growing interest in the alternative splicing mechanisms that affect the functionality of such epigenetic readers in cancer etiology. The current review considers how [...] Read more.
Epigenetic ‘reader’ proteins, which have evolved to interact with specific chromatin modifications, play pivotal roles in gene regulation. There is growing interest in the alternative splicing mechanisms that affect the functionality of such epigenetic readers in cancer etiology. The current review considers how deregulation of epigenetic processes and alternative splicing events contribute to pathophysiology. An A–Z guide of epigenetic readers is provided, delineating the antagonistic ‘yin-yang’ roles of full-length versus spliced isoforms, where this is known from the literature. The examples discussed underscore the key contributions of epigenetic readers in transcriptional regulation, early development, and cancer. Clinical implications are considered, offering insights into precision oncology and targeted therapies focused on epigenetic readers that have undergone alternative splicing events during disease pathogenesis. This review underscores the fundamental importance of alternative splicing events in the context of epigenetic readers while emphasizing the critical need for improved understanding of functional diversity, regulatory mechanisms, and future therapeutic potential. Full article
(This article belongs to the Special Issue Cancer Genetics and Epigenetics: Their Roles and Clinical Implications)
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20 pages, 2350 KiB  
Review
Genetics of ABCB1 in Cancer
by Katie T. Skinner, Antara M. Palkar and Andrew L. Hong
Cancers 2023, 15(17), 4236; https://doi.org/10.3390/cancers15174236 - 24 Aug 2023
Cited by 34 | Viewed by 5129
Abstract
ABCB1, also known as MDR1, is a gene that encodes P-glycoprotein (P-gp), a membrane-associated ATP-dependent transporter. P-gp is widely expressed in many healthy tissues—in the gastrointestinal tract, liver, kidney, and at the blood–brain barrier. P-gp works to pump xenobiotics such as [...] Read more.
ABCB1, also known as MDR1, is a gene that encodes P-glycoprotein (P-gp), a membrane-associated ATP-dependent transporter. P-gp is widely expressed in many healthy tissues—in the gastrointestinal tract, liver, kidney, and at the blood–brain barrier. P-gp works to pump xenobiotics such as toxins and drugs out of cells. P-gp is also commonly upregulated across multiple cancer types such as ovarian, breast, and lung. Overexpression of ABCB1 has been linked to the development of chemotherapy resistance across these cancers. In vitro work across a wide range of drug-sensitive and -resistant cancer cell lines has shown that upon treatment with chemotherapeutic agents such as doxorubicin, cisplatin, and paclitaxel, ABCB1 is upregulated. This upregulation is caused in part by a variety of genetic and epigenetic mechanisms. This includes single-nucleotide variants that lead to enhanced P-gp ATPase activity without increasing ABCB1 RNA and protein levels. In this review, we summarize current knowledge of genetic and epigenetic mechanisms leading to ABCB1 upregulation and P-gp-enhanced ATPase activity in the setting of chemotherapy resistance across a variety of cancers. Full article
(This article belongs to the Special Issue Cancer Genetics and Epigenetics: Their Roles and Clinical Implications)
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