Cancer Genomics: Emerging Trends and Technological Advances

Topic Information

Dear Colleagues,

We are pleased to announce the new Topic “Cancer Genomics: Emerging Trends and Technological Advances”. This initiative aims to foster and integrate cutting-edge research in cancer genetics and genomics, addressing the complexity and heterogeneity of this disease. In recent years, the incorporation of novel technologies into cancer genomics has significantly expanded our understanding of tumor biology, enabling advances in diagnosis, prognosis, and therapeutic strategies. Therefore, this Topic seeks to promote and gather high-quality research that leverages innovative approaches to investigate the genetic and genomic underpinnings of cancer. We particularly welcome original studies and reviews that integrate data from next-generation sequencing (NGS), computational analyses, multi-omics profiling, machine learning algorithms, and other advanced tools to explore cancer susceptibility, progression, and treatment response. By highlighting emerging technologies and interdisciplinary approaches, we hope this Topic will contribute to a more comprehensive and precise understanding of cancer biology and support the development of personalized medicine strategies. We look forward to your valuable contributions.

Dr. Martha Patricia Gallegos-Arreola
Dr. Luis Eduardo Figuera Villanueva
Dr. Hector Barajas-Martinez
Topic Editors

Keywords

Participating Journals

Journal Name	Impact Factor	CiteScore	Launched Year	First Decision (median)	APC
Biomedicines biomedicines	3.9	6.8	2013	21 Days	CHF 2600	Submit
Cancers cancers	4.4	8.8	2009	19.1 Days	CHF 2900	Submit
Current Oncology curroncol	3.4	4.9	1994	22.8 Days	CHF 2200	Submit
Journal of Clinical Medicine jcm	2.9	5.2	2012	18.5 Days	CHF 2600	Submit
Onco onco	-	-	2021	23.7 Days	CHF 1000	Submit

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Published Papers (5 papers)

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All Biomedicines Cancers Current Oncology JCM Onco

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15 pages, 717 KB  

Open AccessSystematic Review

SMARCA4-Deficient Carcinomas of the Small Intestine: A Systematic Review

by Aaqid Syed, Yanis Boumber and Midhun Malla

Curr. Oncol. 2026, 33(2), 107; https://doi.org/10.3390/curroncol33020107 - 10 Feb 2026

Viewed by 146

Abstract

Purpose: SMARCA4-deficient carcinomas are rare, aggressive malignancies characterized by loss of BRG1, a core component of the SWI/SNF chromatin remodeling complex. These typically arise in the chest, but recent case reports suggest rare involvement of the gastrointestinal tract, particularly the small intestine. [...] Read more.

Purpose: SMARCA4-deficient carcinomas are rare, aggressive malignancies characterized by loss of BRG1, a core component of the SWI/SNF chromatin remodeling complex. These typically arise in the chest, but recent case reports suggest rare involvement of the gastrointestinal tract, particularly the small intestine. This review aims to consolidate the available literature on SMARCA4-deficient carcinomas of the small intestine, highlighting their clinical, histopathological, molecular, and therapeutic features. Design: A systematic review of PubMed was conducted through March 2025 to identify all published cases of primary SMARCA4-deficient carcinomas of the small intestine. Inclusion criteria required immunohistochemical or molecular confirmation of SMARCA4/BRG1 loss. Studies describing metastases, non-small intestine primaries, or lacking molecular data were excluded. Ten eligible cases were analyzed in detail. Results: Patients were predominantly male (9 out of 10) with a median age of 54 years. Most carcinomas arose in the duodenum and patients frequently presented with nonspecific symptoms and advanced-stage disease. Histologically, tumors demonstrated undifferentiated or rhabdoid features with high mitotic activity and extensive necrosis. Immunohistochemistry confirmed loss of SMARCA4, while several cases also showed SMARCA2 loss. Molecular profiling revealed congruent mutations in TP53 and CTNNB1, among oncogenic drivers. While some patients with localized disease achieved prolonged survival after surgery and adjuvant chemotherapy, those with metastatic disease had limited responses to immune checkpoint inhibitors, despite PD-L1 positivity in a subset. Overall survival ranged from 2 to 29 months. Conclusions: SMARCA4-deficient carcinomas of the small intestine represent a distinct, high-grade malignancy with poor prognosis and limited therapeutic options. Prompt recognition, SMARCA4 testing, and referral to specialized centers are essential. Prospective studies are needed to guide therapy and explore targeted approaches in this challenging carcinoma subtype. Full article

(This article belongs to the Topic Cancer Genomics: Emerging Trends and Technological Advances)

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52 pages, 2285 KB  

Open AccessReview

Intersection of Precision Nutrition and Bladder Cancer: A Narrative State-of-the-Art Review of Potential Applications and Challenges

by Tevfik Koçak, Yağmur Demirel Özbek, Mahmut Bodur, Süleyman Yeşil and Duygu Ağagündüz

J. Clin. Med. 2026, 15(3), 1247; https://doi.org/10.3390/jcm15031247 - 4 Feb 2026

Viewed by 311

Abstract

Bladder cancer (BC) is a biologically heterogeneous tumor affected by genetic, metabolic, environmental, and lifestyle factors. Recent research indicates that nutrition can change the way urothelial cancer forms by affecting inflammation, oxidative stress, cellular energy, and the epigenome. It can also change the [...] Read more.

Bladder cancer (BC) is a biologically heterogeneous tumor affected by genetic, metabolic, environmental, and lifestyle factors. Recent research indicates that nutrition can change the way urothelial cancer forms by affecting inflammation, oxidative stress, cellular energy, and the epigenome. It can also change the risk of BC and how well treatment works. Simultaneous progress in precision nutrition (PN) and nutriomic profiling—encompassing nutrigenomics, nutrigenetics, nutriepigenetics, metabolomics, and microbiome science—presents novel options to tailor dietary regimens beyond universal guidelines. In this review, we consolidate existing knowledge regarding the nutritional factors influencing BC, outline pertinent principles of PN for BC prevention and survival, and explore how urine proteomics and molecular subtyping facilitate the integration of PN into precision oncology. Our review examines the methodological, bioinformatic, biomarker, and clinical translation challenges that impede the implementation of PN in BC management; these challenges include the need for validated nutritional biomarkers with mechanistic endpoints, interoperable data platforms, and rigorously designed clinical trials. Finally, we emphasize future prospects for PN-guided medical nutrition therapy and dietary models during and after systemic treatment recovery. We propose research priorities that will facilitate the integration of PN-informed individualized dietary plans with medical and surgical approaches in BC treatment, aiming to decrease the costs associated with expensive or excessively aggressive treatment methods, thereby supporting long-term survival care. This review seeks to establish a conceptual framework for the integration of PN into BC management by delineating the opportunities and challenges, hence promoting hypothesis-driven research in a promising yet underexplored domain. Full article

(This article belongs to the Topic Cancer Genomics: Emerging Trends and Technological Advances)

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14 pages, 495 KB  

Open AccessReview

Strategies for the Molecular Classification of Medulloblastoma

by Josselen Carina Ramírez-Chiquito and Sergio Juárez-Méndez

Biomedicines 2025, 13(12), 2845; https://doi.org/10.3390/biomedicines13122845 - 21 Nov 2025

Viewed by 1049

Abstract

Fifteen years ago, an omic study of medulloblastoma revealed the existence of four groups that are biologically and clinically different. Since then, various molecular classification methods have emerged, each with different diagnostic capabilities. Knowledge of these tools is essential for countries with low [...] Read more.

Fifteen years ago, an omic study of medulloblastoma revealed the existence of four groups that are biologically and clinically different. Since then, various molecular classification methods have emerged, each with different diagnostic capabilities. Knowledge of these tools is essential for countries with low economic resources to be able to access the technology that is most within their reach since, at present, the precision of molecular classification is crucial for clinical practice, not only because of its relevance in the prognosis of patients but also because of its decisive impact on therapeutic strategies, which are essential for reducing mortality from this disease. Full article

(This article belongs to the Topic Cancer Genomics: Emerging Trends and Technological Advances)

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17 pages, 641 KB  

Open AccessReview

Evolving Therapeutic Landscape of ROS1-Positive Non-Small Cell Lung Cancer: An Updated Review

by Hervé Bischoff, Sébastien Gendarme, Laura Somme, Christos Chouaid and Roland Schott

Curr. Oncol. 2025, 32(11), 626; https://doi.org/10.3390/curroncol32110626 - 6 Nov 2025

Cited by 1 | Viewed by 2417

Abstract

ROS1 gene rearrangements define a distinct molecular subtype of non-small cell lung cancer (NSCLC), occurring in approximately 2% of cases and frequently associated with younger age, non-smoker status, and a high incidence of brain metastases. The discovery of ROS1 as an oncogenic driver [...] Read more.

ROS1 gene rearrangements define a distinct molecular subtype of non-small cell lung cancer (NSCLC), occurring in approximately 2% of cases and frequently associated with younger age, non-smoker status, and a high incidence of brain metastases. The discovery of ROS1 as an oncogenic driver has led to the development of targeted tyrosine kinase inhibitors (TKIs). Crizotinib first demonstrated substantial clinical benefit, but its limitations, including poor central nervous system (CNS) penetration and acquired resistance, highlighted the need for next-generation inhibitors. Several agents have since been developed, including entrectinib, lorlatinib, repotrectinib, taletrectinib, and zidesamtinib, each offering improved intracranial (IC) activity and efficacy against resistance mutations, notably ROS1^G2032R. Despite these advances, optimal sequencing strategies remain undefined, and resistance ultimately emerges in most patients. This review provides an updated overview of ROS1 biology, diagnostic approaches, clinical outcomes with currently available TKIs, mechanisms of resistance, and ongoing challenges, emphasizing the rapidly evolving therapeutic landscape. Full article

(This article belongs to the Topic Cancer Genomics: Emerging Trends and Technological Advances)

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14 pages, 1354 KB  

Open AccessArticle

CRISPR with a Double Mismatch Guide RNA Enhances Detection Sensitivity for Low-Frequency Single-Base EGFR Mutation in Circulating Cell-Free DNA of Lung Cancer Patients

by Kyung Wook Been, Seunghun Kang, Taegeun Bae, Sumin Hong, Garyeong Kim, Junho K. Hur, Woochang Hwang and Boksoon Chang

Cancers 2025, 17(20), 3343; https://doi.org/10.3390/cancers17203343 - 16 Oct 2025

Viewed by 1051

Abstract

Background/Objectives: Liquid biopsy using cfDNA has emerged as a promising, minimally invasive alternative to traditional tissue biopsy for detecting cancer-associated mutations. However, the extremely low proportion of mutant DNA in cfDNA poses a major challenge for accurate detection, especially when using conventional sequencing [...] Read more.

Background/Objectives: Liquid biopsy using cfDNA has emerged as a promising, minimally invasive alternative to traditional tissue biopsy for detecting cancer-associated mutations. However, the extremely low proportion of mutant DNA in cfDNA poses a major challenge for accurate detection, especially when using conventional sequencing methods. To address this limitation, we sought to develop a highly sensitive diagnostic strategy to selectively enrich rare mutant sequences and improve the detection of clinically important mutations in patients with NSCLC. Methods: We established a CRISPR/Cas12a-based diagnostic system designed to selectively cleave WT DNA, thereby increasing the relative abundance of mutant DNA in cfDNA samples. Following Cas12a-mediated WT cleavage, the remaining DNA was subjected to PCR amplification for mutation identification. The system was applied to plasma cfDNA from blood samples of 48 NSCLC patients to evaluate its ability to detect two major EGFR mutations: L858R and exon 19 deletion. Results: The CRISPR/Cas12a-based diagnostic system effectively identified low-frequency EGFR mutations in cfDNA. Specifically, all 7 L858R-positive samples and 6 out of 11 samples harboring exon 19 deletions—previously validated through tissue biopsy—were successfully detected. This demonstrated a high degree of concordance between our liquid biopsy approach and conventional diagnostic methods. Conclusions: Our findings highlight the potential of the CRISPR/Cas12a-based mutation enrichment system as a powerful tool for detecting rare oncogenic mutations in liquid biopsy samples. This technique enhances diagnostic sensitivity and could be broadly applicable for the non-invasive detection of various genetic alterations in cancer and other diseases. Full article

(This article belongs to the Topic Cancer Genomics: Emerging Trends and Technological Advances)

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