Genes, Chromosomes & Cancer最新文献

{"title":"Chromatin Interaction and Histone Mark Signatures Associated With TBXT Expression in Metastatic Lung Cancer","authors":"Reuben M. Yaa,&nbsp;Brian M. Schilder,&nbsp;Rafael D. Acemel,&nbsp;Fiona C. Wardle","doi":"10.1002/gcc.70041","DOIUrl":"https://doi.org/10.1002/gcc.70041","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Background</h3>\u0000 \u0000 <p><i>TBXT,</i> a member of the T-box transcription factor family, drives epithelial-to-mesenchymal transition in the metastasis of some cancers. However, the relationship between the epigenetic regulatory landscape and its expression in lung cancers remains elusive.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>Circularized chromosome capture combined with sequencing (4C-seq) was employed to analyze physical chromatin interactions at the <i>TBXT</i> loci in the lung cancer cell line H460, a high <i>TBXT-expressing</i> cell line, compared to H358 and A549, which do not express <i>TBXT</i>. To define the regulatory landscape, the targeted <i>TBXT</i> chromatin interactions were integrated with histone modification profiles from respective cells, followed with motif analysis.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Our analysis identified distinct patterns of potential <i>cis</i>-regulatory elements (pCREs) associated with the <i>TBXT</i> promoter, with increased near-<i>cis</i> pCRE enrichment in the <i>TBXT-expressing</i> cells. Integration of pCREs with epigenetic histone modification revealed two unique pCREs in <i>TBXT-expressing</i> H460 cells enriched with the active histone mark H3K27ac, harboring binding sites for transcription factors of the forkhead box, zinc finger, and musculoaponeurotic fibrosarcoma families that are linked to cancer metastasis.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusion</h3>\u0000 \u0000 <p>Our findings shed light on active chromatin interactions with <i>TBXT</i> expression in lung cancers, pointing to specific DNA elements and regulatory proteins that may be involved. This knowledge paves the way for understanding <i>TBXT</i> expression dynamics at the onset and progression of metastatic cancers.</p>\u0000 </section>\u0000 </div>","PeriodicalId":12700,"journal":{"name":"Genes, Chromosomes & Cancer","volume":"64 3","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/gcc.70041","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143639316","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"EWSR1::CREM Fusion in a Pediatric Patient With Testicular Leydig Cell Tumor","authors":"Megan M. Lilley,&nbsp;Patrick R. Blackburn,&nbsp;Larissa V. Furtado,&nbsp;Alberto S. Pappo,&nbsp;Selene C. Koo","doi":"10.1002/gcc.70038","DOIUrl":"https://doi.org/10.1002/gcc.70038","url":null,"abstract":"<div>\u0000 \u0000 <p>Sex cord-stromal tumors are rare in pediatric patients. Leydig cell tumors are a rare subset of sex cord-stromal tumors characterized by unique molecular alterations, including <i>TERT</i> fusions and mutations of <i>CTNNB1</i>, <i>FOXO4</i>, <i>TP53, NBN, MTOR, BAP1, MEN1,</i> and <i>CREBBP</i>. We report a case of a testicular Leydig cell tumor with an <i>EWSR1::CREM</i> fusion, which to our knowledge has not been previously reported in this setting.</p>\u0000 </div>","PeriodicalId":12700,"journal":{"name":"Genes, Chromosomes & Cancer","volume":"64 3","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143595405","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"FIP1L1::PDGFRA Fusion in a Pediatric Patient Presenting With B-Cell Lymphoblastic Leukemia","authors":"Jenna Nunn,&nbsp;Bronwyn Williams,&nbsp;David Deambrosis","doi":"10.1002/gcc.70037","DOIUrl":"https://doi.org/10.1002/gcc.70037","url":null,"abstract":"<p>Approximately 10% of Ph-Like patients have <i>ABL</i> class gene fusions, which include the <i>FIP1L1::PDGFRA</i> rearrangement. We report a case of a pediatric patient with Ph-like B-lymphoblastic leukemia (B-LL) with a <i>FIP1L1::PDGFRA</i> fusion and their treatment course using a combination of chemotherapy and targeted therapy with imatinib. A 10-year-old female presented with lethargy, palpitations, and fevers. She had pancytopenia, no eosinophilia, and flow cytometry consistent with B-LL. FISH identified a <i>CHIC2</i> deletion, suggestive of <i>FIP1L1::PDGFRA</i> fusion, confirmed on next-generation RNA sequencing. The patient commenced targeted therapy with imatinib, which she continued until completion of standard chemotherapy per COG AALL1732. She remains in remission 6 months post-completion of therapy. B-ALL with a <i>FIP1L1::PDGFRA</i> fusion is extremely rare, particularly in pediatrics. <i>FIP1L1::PDGFRA</i> rearrangements can be difficult to detect on routine testing and may not always be seen in association with eosinophilia. Identification of <i>FIP1L1::PDGFRA</i> rearrangements is important as they enable treatment with a tyrosine kinase inhibitor, which has significantly improved the overall prognosis for <i>PDGFRA</i>-rearranged neoplasms. Prospective studies assessing imatinib dosage, duration, and long-term safety are warranted in this cohort.</p>","PeriodicalId":12700,"journal":{"name":"Genes, Chromosomes & Cancer","volume":"64 2","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/gcc.70037","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143481594","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Schwann Cells Deficient in Neurofibromin Lack Sensitivity to Their Biomechanical Microenvironment","authors":"Micah Rambo,&nbsp;Isheka Agarwala,&nbsp;Camdyn Vanek,&nbsp;Yuxin Xiao,&nbsp;Emma Brown,&nbsp;K. L. Mills","doi":"10.1002/gcc.70036","DOIUrl":"https://doi.org/10.1002/gcc.70036","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Background and Aims</h3>\u0000 \u0000 <p>Plexiform neurofibromas (PNFs) are benign tumors of the peripheral nervous system that affect approximately 30% of people with neurofibromatosis type 1 (NF1). Schwann cells (SCs), the tumor progenitor cells, respond to and use biomechanical signals like tissue stiffness and mechanical loads in their maintenance and repair functions in healthy tissues. PNFs are described as having altered biomechanics, and we hypothesize this plays a role in PNF development. As a first step in studying the role that altered biomechanics may play in the development of PNFs, we aimed to determine how PNF SCs alter in their response to various biomechanical signals as compared to healthy SCs.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We examined the behavior of healthy and PNF SCs in three different tissue-mimicking biomechanical models. First, we examined their spreading behavior on extracellular matrix (ECM) protein-coated polyacrylamide hydrogels of varying stiffness in the healthy and pathological range. Second, we investigated their collective migration with respect to substrate stiffness and ECM protein-coating. Finally, we generated multicellular spheroid tissue models using healthy and PNF SCs and measured their mechanical properties as a function of spheroid size.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>We found that PNF SCs are differently sensitive to substrate stiffness in a physiological range compared to healthy SCs, lack sensitivity to ECM protein coating when collectively migrating, and lack sensitivity to environmental deficiencies in oxygen and nutrient supplies when in spheroid culture.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Interpretation</h3>\u0000 \u0000 <p>We propose that PNF SC altered biomechanics likely play a role in tumor initiation and progression, and that further biomechanical-based investigations of NF1 tumor growth are needed.</p>\u0000 </section>\u0000 </div>","PeriodicalId":12700,"journal":{"name":"Genes, Chromosomes & Cancer","volume":"64 2","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143481593","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pregnancy and the Risk for Cancer in Neurofibromatosis 1","authors":"Roope A. Kallionpää,&nbsp;Juha Määttänen,&nbsp;Jussi Leppävirta,&nbsp;Sirkku Peltonen,&nbsp;Juha Peltonen","doi":"10.1002/gcc.70017","DOIUrl":"https://doi.org/10.1002/gcc.70017","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Background</h3>\u0000 \u0000 <p>Neurofibromatosis type 1 (NF1) is associated with a high risk for cancer. Benign cutaneous neurofibromas of women with NF1 may increase in size and number during pregnancy. However, it is not known whether pregnancy affects the risk for cancer in NF1.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We retrieved the pregnancies of women in the Finnish NF1 cohort and in a 10-fold control cohort from the Finnish Medical Birth Register. Cancers occurring during or after pregnancy were obtained from the Finnish Cancer Registry and summarized using standardized incidence ratio (SIR). The cancer incidence of nonNF1 mothers of individuals with NF1 was also estimated.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Totals of 263 pregnancies in 136 women with NF1 and 3176 pregnancies in 1720 controls were observed. In the NF1 group, two cancers were identified during pregnancy and the year following the delivery (SIR 6.44, 95% CI 1.07–19.89). Among controls, the SIR was markedly lower (0.25, 95% CI 0.01–1.08). Within 1–10 years after pregnancy, the SIR of women with NF1 was 7.54 (95% CI 4.15–12.41). The SIR of women with NF1 aged 20–49 years, and without a known history of deliveries was 8.63 (95% CI 6.08–11.81). The nonNF1 mothers displayed a SIR of 0.81 (95% CI 0.66–1.00) after giving birth to a child with NF1.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>The pregnancy-related cancer incidence in women with NF1 is similar to women with NF1 aged 20–49 years overall, although notably higher than in the general population. Giving birth to a child with NF1 does not affect the risk for cancer in women without NF1.</p>\u0000 </section>\u0000 </div>","PeriodicalId":12700,"journal":{"name":"Genes, Chromosomes & Cancer","volume":"64 2","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/gcc.70017","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143466067","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A MAZ::NCOA2 Subcutaneous Small Round Cell Sarcoma of Infancy With Diffuse S100/SOX10 Positivity: A Novel Entity","authors":"Huiyao Chen,&nbsp;Pu Zhang,&nbsp;Lingli Zhou","doi":"10.1002/gcc.70034","DOIUrl":"https://doi.org/10.1002/gcc.70034","url":null,"abstract":"<div>\u0000 \u0000 <p>Small round cell sarcomas (SRCSs) constitute a heterogeneous group of high-grade tumors with a poor prognosis, predominantly affecting children and young adults. According to the 2020 WHO Soft Tissue Tumor classification, SRCSs are categorized into Ewing sarcoma, round cell sarcoma with <i>EWSR1</i>-non-ETS fusions, <i>CIC</i>-rearranged sarcoma, and sarcoma with <i>BCOR</i> genetic alterations. Herein, we report a case of a 10-month-old boy presenting with a progressively enlarging left lumbar mass. Histopathological examination revealed a well-demarcated lesion composed of small, round to oval cells with scant cytoplasm and mildly irregular nuclei. Immunohistochemical staining demonstrated strong, diffuse positivity for S100 and SOX10, indicating neurocristic differentiation. Next-generation sequencing identified an in-frame fusion between <i>MAZ</i> exon 3 on chromosome 16 and <i>NCOA2</i> exon 12 on chromosome 8. Fluorescence in situ hybridization (FISH) confirmed a break-apart signal at the <i>NCOA2</i> locus. To the best of our knowledge, this represents the first documented instance of an <i>NCOA2</i> rearrangement involving <i>MAZ</i> in SRCSs. This case broadens the molecular spectrum of SRCSs, highlights the importance of incorporating molecular techniques into diagnostic workflows, and may have implications for future diagnostic and therapeutic strategies.</p>\u0000 </div>","PeriodicalId":12700,"journal":{"name":"Genes, Chromosomes & Cancer","volume":"64 2","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143466068","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"PDGFRA::USP8 Fusion in a Cutaneous Inflammatory Myofibroblastic Tumor, Highlighting Genetic Pleiotropy of Kinase Gene Fusions in Soft Tissue Neoplasms","authors":"Astrid I. P. Vernemmen,&nbsp;Léon C. L. T. van Kempen,&nbsp;Frits Aarts,&nbsp;Axel zur Hausen,&nbsp;Raf M. E. Sciot,&nbsp;Jason L. Hornick,&nbsp;Mari F. C. M. van den Hout","doi":"10.1002/gcc.70035","DOIUrl":"https://doi.org/10.1002/gcc.70035","url":null,"abstract":"<p><i>PDGFRA::USP8</i> fusions have recently been described in neoplasms in the provisional category of calcified chondroid mesenchymal neoplasm (CCMN). Here, we describe a cutaneous inflammatory myofibroblastic tumor (IMT) on the upper leg of a 24-year-old male harboring the same fusion product. The tumor showed a morphology typical of IMT, including a concomitant inflammatory infiltrate; in addition, there was strong immunohistochemical PDGFRα overexpression. Methylation profiling (Sarcoma classifier v12.2) was consistent with IMT (calibrated score 0.99). Herein, we review other soft tissue tumors with <i>PDGFRA</i> fusions, emphasizing <i>PDGFRA::USP8</i> fusions, further highlighting the genetic pleiotropy of kinase gene fusions in soft tissue tumors. In addition, this case expands the landscape of kinase fusions in IMT, presented by an extremely rare cutaneous IMT.</p>","PeriodicalId":12700,"journal":{"name":"Genes, Chromosomes & Cancer","volume":"64 2","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/gcc.70035","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143404576","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Novel ACVR2A::RAF1 Fusion in Spindle Cell Sarcoma","authors":"Anfeng Jiang,&nbsp;Huan Li,&nbsp;Dongbing Li,&nbsp;Huafei Chen,&nbsp;Lina Zhao,&nbsp;Ying Zhang,&nbsp;Yangyang Li,&nbsp;Rong Rong,&nbsp;Bin Li,&nbsp;Sheng Xiao","doi":"10.1002/gcc.70033","DOIUrl":"https://doi.org/10.1002/gcc.70033","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Background</h3>\u0000 \u0000 <p>Kinase-rearranged spindle cell sarcomas are characterized by unique molecular features. The advent of next-generation sequencing (NGS) has enabled the detection of a multitude of kinase fusions, thereby contributing to the accurate categorization of these tumors.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Case Presentation</h3>\u0000 \u0000 <p>A 37-year-old woman experienced the fourth recurrence of a cranial base tumor 25 years following the initial surgery and radiation therapy. Histological analysis disclosed spindle-shaped and oval tumor cells, along with a high number of mitotic figures. Immunohistochemistry showed a null immunophenotype, negative for pan-TRK, S-100, CD34, pan-CK, GFAP, and Olig2. Molecular analysis of the tumor tissue identified a novel ACVR2A::RAF1 fusion, comprising the first four exons of ACVR2A and the last nine exons of RAF1. The resulting fusion protein retains the extracellular and transmembrane domains of ACVR2A, while its kinase domain is replaced by the kinase domain of RAF1. This hybrid protein likely contributes to tumorigenesis by activating RAF1 signaling in response to ACVR2A ligands from the TGF-β superfamily.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Treatment and Outcome</h3>\u0000 \u0000 <p>The patient was treated with the MEK1 inhibitor Trametinib, 2 mg per time and once a day. One month later, MRI showed significant tumor shrinkage and pain relief.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusion</h3>\u0000 \u0000 <p>The ACVR2A::RAF1 fusion represents a novel genomic profile in RAF1-rearranged spindle cell sarcoma, offering a rational basis for targeted therapy. This case highlights the importance of molecular diagnostics in identifying actionable targets and guiding treatment, potentially leading to significant clinical benefits.</p>\u0000 </section>\u0000 </div>","PeriodicalId":12700,"journal":{"name":"Genes, Chromosomes & Cancer","volume":"64 2","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143404577","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Challenging Conventional Perceptions of Oncogenes and Tumor Suppressor Genes: A Comprehensive Analysis of Gene Expression Patterns in Cancer","authors":"Mingyuan Zou,&nbsp;Li Qiu,&nbsp;Wentao Wu,&nbsp;Hui Liu,&nbsp;Han Xiao,&nbsp;Jun Liu","doi":"10.1002/gcc.70030","DOIUrl":"https://doi.org/10.1002/gcc.70030","url":null,"abstract":"<div>\u0000 \u0000 <p>Identifying genes involved in cancer is crucial for understanding the underlying molecular mechanisms of the disease and developing effective treatment strategies. Differential expression analysis (DEA) is the predominant method used to identify cancer-related genes. This approach involves comparing gene expression levels between different samples, such as cancerous and non-cancerous tissues, to identify genes that are significantly upregulated or downregulated in cancer. DEA is based on the commonly believed assumption that genes upregulated in cancerous tissues have the potential to function as oncogenes. Their expression levels often correlate with cancer advancement and unfavorable prognosis, whereas downregulated genes display the opposite correlation. However, contrary to the prevailing belief, our analysis utilizing The Cancer Genome Atlas (TCGA) databases revealed that the upregulated or downregulated genes in cancer do not always align with cancer progression or prognosis. These findings emphasize the need for alternative approaches for identifying cancer-related genes that may be more accurate and effective. To address this need, we compared the effectiveness of machine learning (ML) methods with that of traditional DEA in the identification of cancer-related genes. ML algorithms have the advantage of being able to analyze large-scale genomic data and identify complex patterns that may go unnoticed by traditional methods. Our results demonstrated that ML methods significantly outperformed DEA in the screening of cancer-related genes.</p>\u0000 </div>","PeriodicalId":12700,"journal":{"name":"Genes, Chromosomes & Cancer","volume":"64 2","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143389279","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Profiling Precursor microRNAs of Breast Cancer From Total RNA Sequencing Data to Gain Insights Into Their Roles and Prognostic Values","authors":"Sen Wu,&nbsp;Jia-Wern Pan,&nbsp;Marimuthu Citartan,&nbsp;Thean-Hock Tang,&nbsp;MyBrCa Collaborative Group,&nbsp;Soo-Hwang Teo,&nbsp;Ewe Seng Ch'ng","doi":"10.1002/gcc.70027","DOIUrl":"https://doi.org/10.1002/gcc.70027","url":null,"abstract":"<div>\u0000 \u0000 <p>Breast cancer, a molecularly heterogeneous disease, is classified into hormone receptor-positive luminal breast cancer (LBC), human epidermal growth factor receptor 2-positive breast cancer, and triple-negative breast cancer (TNBC). Precursor microRNAs (pre-miRNAs), typically form hairpin structures with a length from 65 to 80 bases, are shown to play crucial roles in breast cancer carcinogenesis. We hypothesized that these pre-miRNAs could have been sequenced in total RNA sequencing (RNA-seq) and developed a novel algorithm to profile pre-miRNAs from raw total RNA-seq data. A total of 907 breast cancer samples curated by Malaysian Breast Cancer Genetic Study (MyBrCa) were profiled using this algorithm and a comparison was made between pre-miRNA profiles and mature miRNA profiles obtained from The Cancer Genome Atlas (TCGA) dataset. We explored differentially expressed pre-miRNAs in TNBC in comparison to LBC and conducted downstream functional analyses of the target genes. A prognostic signature was built by LASSO–Cox regression on selected pre-miRNAs and validated internally and externally by MyBrCa and TCGA datasets, respectively. As a result, 10 common differentially expressed pre-miRNAs were identified. Functional analyses of these pre-miRNAs captured certain aggressive TNBC behaviors. Importantly, a pre-miRNA signature composed of 4 out of these 10 pre-miRNAs significantly prognosticated the breast cancer patients in the MyBrCa cohort and TCGA cohort, independent of conventional prognostic factors. In conclusion, this novel algorithm allows profiling pre-miRNAs from raw total RNA-seq data, which could be cross-validated with mature miRNA profiles for cross-platform comparison. The findings of this study underscore the importance of pre-miRNAs in breast cancer carcinogenesis and as prognostic factors.</p>\u0000 </div>","PeriodicalId":12700,"journal":{"name":"Genes, Chromosomes & Cancer","volume":"64 2","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143389278","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}