Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal

Interallelic gene conversion of leukemia-associated single nucleotide variants

CRISPR-Cas9 is a useful tool for inserting precise genetic alterations through homology-directed repair (HDR), although current methods largely rely on provision of an exogenous repair template. Here, we tested the possibility of interchanging heterozygous single nucleotide variants (SNVs) using mutation-specific guide RNA, and the cell's own wild-type allele rather than an exogenous template. Using high-fidelity Cas9 to perform allele-specific CRISPR across multiple human leukemia cell lines as well as in primary hematopoietic cells from patients with leukemia, we find high levels of reversion to wild-type in the absence of exogenous template. Moreover, we demonstrate that bulk treatment to revert a truncating mutation in ASXL1 using CRISPR-mediated interallelic gene conversion (IGC) is sufficient to prolong survival in a human cell line-derived xenograft model (median survival 33 days vs 27.5 days; p = 0.0040). These results indicate that IGC is a useful laboratory tool which can be applied to numerous types of leukemia and can meaningfully alter cellular phenotypes at scale. Because our method targets single-base mutations, rather than larger variants targeted by IGC in prior studies, it greatly expands the pool of genetic lesions which could potentially be targeted by IGC. This technique may reduce cost and complexity for experiments modeling phenotypic consequences of SNVs. The principles of SNV-specific IGC demonstrated in this proof-of-concept study could be applied to investigate the phenotypic effects of targeted clonal reduction of leukemogenic SNV mutations.

MK2 promotes p16 negative head and neck cancer migration, invasion, and metastasis

For patients with locally advanced, p16-negative head and neck squamous cell carcinoma (HNSCC), overall survival remains poor due to primary locoregional failure and distant metastasis following curative therapy. We aimed to understand how MAPKAPK2 (MK2) regulates HNSCC tumor cell migration and invasion, important first steps in cancer metastases. The TCGA database and HNSCC tissue microarrays were used to show that MK2 expression was associated with more advanced cancers and faster cancer recurrence rates. We observed that silencing of tumor MK2 in human cell lines (shRNA) caused a significant reduction in tumor cell migration-invasion in a complex HNSCC microphysiologic system used to recapitulate the tumor microenvironment. Murine cells (Ly2) with MK2 silenced (CRISPR-Cas9) also demonstrated reduced migration and invasion using 2D and 3D monoculture cell migration-invasions assays. Ly2 cells are orthotopic p16-negative murine metastatic cells that spontaneously metastasize, and we observed that MK2 inhibition via genetic (Cas9/CRISPR) or pharmacologic (PF-3644022) methods led to a significant reduction in the number of circulating tumor cells, fewer lymph node and lung metastases, and MK2 inhibited mice showed improved overall survival. Our findings suggest that HNSCC MK2 regulates tumor cell migration-invasion and may be a promising therapeutic target to reduce metastases.

Nicotinamide metabolism affects the prognosis of hepatocellular carcinoma by influencing the tumor microenvironment

In this study, we utilized the public database along with single-cell genomics techniques to systematically analyze the expression patterns and clinical significance of key genes in the nicotinamide metabolism pathway in liver cancer samples. The findings indicate that differential nicotinamide metabolism-related key genes are expressed in liver cancer samples. The liver cancer samples were put into separate subgroups using consistency clustering analysis based on differential gene expression levels observed. Additionally, immune infiltration and drug sensitivity analysis also revealed differences between the two subgroups. Survival analysis suggested that the key genes were associated with prognosis. Finally, a prognostic model was established using the key genes, offering a fresh viewpoint on the molecular mechanism investigating liver cancer. This study demonstrated the significant correlation between key genes in the nicotinamide metabolism pathway and the occurrence and progression of liver cancer and indicated that these key genes could serve as prognostic markers and tailored treatment targets for liver cancer.

Molecular profile of adult primary leptomeningeal gliomatosis aligns with glioblastoma, IDH-wildtype

Adult primary leptomeningeal gliomatosis (PLG) is a rare, rapidly progressive and fatal disease characterized by prominent leptomeningeal infiltration by a glial tumor without an identifiable parenchymal mass. The molecular profile of adult PLG has not been well-characterized. We report the clinical, pathological, and molecular findings of six adult PLG patients (five males and one female), median age 58 years. All cases exhibited pathological leptomeningeal enhancement at presentation. Leptomeningeal biopsy was diagnostic in five (of six) cases, revealing infiltration by an astrocytic glioma with mitotic activity, lacking microvascular proliferation or necrosis. One case was diagnosed at autopsy. All tumors were IDH-wildtype, with five harboring TERT promoter mutations. Additional mutations identified were PTEN in one case, TP53 in two cases, and NF1 in two cases. A chromosome profile with +7/-10 was found in four cases, whereas the remaining two showed either chromosome 7 or 7p gain only. Four cases showed chromosome 9p loss with CDKN2A/B homozygous deletion, one case showed hemizygous CDKN2A/B loss, and one case showed intact chromosome 9 and CDK4/GLI1 amplification. DNA methylation profiling was performed in four cases and revealed a match to glioblastoma (GBM) family and mesenchymal typical class with high confidence scores in two cases; the other two cases showed only suggestive combined scores for GBM family and mesenchymal atypical class. The molecular profile of all cases closely aligned with that of adult-type GBM, IDH-wildtype, CNS WHO grade 4. All patients succumbed to the disease. In five cases with extensive leptomeningeal disease at diagnosis, the course was rapid, with median survival of 24 days following palliative care. Only one case, with relatively localized disease at diagnosis, received chemoradiation therapy and survived 535 days, raising the possibility that early diagnosis and timely treatment could improve outcome. A detailed list of previously reported cases is provided in a supplementary table.

CDX2 downregulation regulates intrinsic WNT pathway activation, dictating metastasis in APC and CTNNB1 wildtype colorectal cancer

Colorectal cancer (CRC) can be divided into 4 subtypes of which consensus molecular subtype 4 (CMS4) is associated with metastasis and poor survival. Previously, we reported that the KPN mouse model resembles human CMS4. Strikingly, although tumor formation in this model is slow and limited, effective metastasis is observed. To understand this aggressive behavior, we compared two distinct in vitro KPN models, organoids and tumoroids. The organoid model only carries the original mutations, while the tumoroids are derived from in vivo grown tumors that underwent selection during development. Here, we reveal that tumoroids harbor endogenous WNT pathway activity, which can be driven by tankyrase activity and Cdx2 downregulation. Importantly, WNT pathway activation was heterogeneous in nature, subject to regulation and allowed for a mixture of WNT-driven and YAP-driven cells within tumoroids. This unique type of WNT pathway activation is not crucial for colonic tumor growth, but results in metastatic spreading. Intriguingly, these findings reflect a specific subset of aggressive human CMS4 cancers that display low CDX2 expression and lack of classical WNT pathway mutations, while having a higher tendency to metastasize. Together, these data propose a novel mechanism for WNT pathway activation that drives metastasis formation in aggressive CRC.

SETDB1 decline promotes the resistance to sorafenib via DRP1 phosphorylation-mediated mitochondrial dysfunction in HepG2 cells

Sorafenib is a widely-adopted kinase inhibitor in anticancer therapy for advanced hepatocellular carcinoma (HCC) and the individualized pharmacological resistance to sorafenib is still an unresolved issue. Whether histone H3K9 methyltransferase SETDB1, which represses chromatin states and promotes various oncogenesis, modulate this process is still elusive. The analysis from both TCGA-LIHC cohort and our clinical HCC patient samples revealed that hepatic SETDB1 expression positively correlates with the prognosis of HCC patients receiving sorafenib therapy. Meanwhile, SETDB1 silencing diminished the cytotoxic effects of sorafenib in hepatoma cells. Mechanistically, SETDB1 knockdown led to mitochondrial dysfunction, including reduced mitochondrial membrane potential, mitochondria superoxide (mSOX), mitochondrial DNA (mtDNA) content, increased fission and DRP1S616 phosphorylation (pDRP1S616) in HepG2 cells. Not only did mSOX fluctuation modulate the sensitivity to sorafenib, but DRP1 activity-silenced counterpart pDRP1S616A inactivation also elevated the susceptibility to sorafenib and the corresponding mSOX and mtDNA content. Finally, pDRP1S616 IHC staining in clinical samples showed that hepatic pDRP1S616 level negatively correlates with the prognosis of HCC patients with sorafenib therapy as well. We first demonstrated that SETDB1 knockdown reduced the susceptibility to sorafenib through enhancing mitochondrial pDRP1S616 in hepatoma cells and hepatic SETDB1 expression might be a potential indicator for clinical HCC sorafenib therapy.

Identification of KANK1 as a tumor suppressor gene in pancreatic ductal adenocarcinoma

Pancreatic cancer is a highly lethal malignancy with poor survival outcomes, primarily due to late-stage diagnosis and resistance to conventional therapies. Identifying key oncogenes and tumor suppressor genes is therefore critical for the development of effective treatment strategies. In this study, we identified KANK1 as a novel tumor suppressor gene in pancreatic ductal adenocarcinoma (PDAC) through an integrated mRNA-protein abundance correlation analysis. Elevated KANK1 expression was consistently associated with improved patient survival across multiple datasets, whereas its expression was markedly reduced in pancreatic tumors compared to normal tissues. Single-cell RNA sequencing and immunoblot analyses confirmed the downregulation of KANK1 at both the mRNA and protein levels in PDAC. Further investigation revealed that KANK1 downregulation is driven by copy number loss and tumor hypoxia, supported by data from the TCGA and CCLE databases and validated experimentally under hypoxic conditions. Functional assays demonstrated that KANK1 knockdown promotes pancreatic cancer cell proliferation and migration, along with activation of ERK signaling. Collectively, our findings establish KANK1 as a tumor suppressor in PDAC, whose loss facilitates tumor progression and presents a potential therapeutic target for pancreatic cancer treatment.

Targeted inhibition of Ninjurin2 promotes chemosensitivity in chemoresistant gastric cancer by suppressing cancer-initiating cells

BACKGROUND

The combination of epirubicin, cisplatin, and 5-fluorouracil (ECF) is widely used for gastric cancer treatment. However, cancer cells can acquire chemoresistance over multiple treatment cycles, leading to recurrence. This study aimed to investigate a novel biomarker for predicting ECF resistance and its biological roles in gastric cancer.

METHODS

ECF-resistant (ECF-R) gastric cancer cell lines were established through stepwise ECF treatment. Transcriptome analysis was performed to identify resistance-related genes, which were validated in tumor organoids and in vivo models. Additionally, gastric cancer patient tumor tissues were analyzed for clinical relevance.

RESULTS

Transcriptome analysis revealed that NINJURIN2 and CD44 were highly expressed in ECF-R cells but rarely expressed in normal gastric tissues. NINJURIN2 inhibition significantly increased chemosensitivity to ECF in vitro and in vivo. Liquid chromatography-tandem mass spectrometry identified periostin as a binding partner of NINJURIN2, mediating chemoresistance. Furthermore, VAV2 phosphorylation was markedly upregulated in ECF-R cells but was inhibited by NINJURIN2 knockdown. Clinical analysis showed that high NINJURIN2 expression correlated with poor survival outcomes in gastric cancer patients.

CONCLUSION

Our findings suggest that NINJURIN2 can be used as a novel biomarker for chemoresistant gastric cancer patients and that inhibiting NINJURIN2 along with standard chemotherapy could prevent chemoresistance-associated relapse in gastric cancer.

Identification and validation of extracellular matrix-related genes in the progression of gastric cancer with intestinal metaplasia

BACKGROUND

Gastric cancer (GC) is a highly lethal malignancy with a high incidence and mortality rate globally. Its development follows the Correa model, with intestinal metaplasia (IM) being a critical precursor to GC. However, the mechanisms underlying IM progression to GC remain unclear. This study explored extracellular matrix (ECM)-related gene changes during IM progression to GC, aiming to identify biomarkers that could improve early diagnosis and treatment strategies for GC, ultimately enhancing patient outcomes.

AIM

To analyze transcriptome sequencing data, molecular biomarkers that can predict GC risk and monitor IM progression can be identified, providing new insights and strategies for preventing IM-GC transformation.

METHODS

Weighted gene co-expression network analysis served for confirming gene modules. Upregulated ECM-related genes were further tested using univariate Cox regression and least absolute shrinkage and selection operator analysis to select hub genes and construct a survival analysis model. The intestinal cell model was established by stimulating GES-1 cells with chenodeoxycholic acid.

RESULTS

Weighted gene co-expression network analysis identified 1709 differentially expressed genes from the GSE191275 dataset, while The Cancer Genome Atlas stomach adenocarcinoma revealed 4633 differentially expressed genes. The intersection of these datasets identified 71 upregulated and 171 downregulated genes, which were enriched in ECM-related pathways. Univariate Cox regression analysis identified six genes with prognostic significance, and least absolute shrinkage and selection operator regression pinpointed secreted protein acidic and rich in cysteine (SPARC) and SERPINE1 as non-zero coefficient genes. A prognostic model integrating clinical tumor node metastasis staging, age, SERPINE1, and SPARC was constructed. Immunohistochemistry analysis confirmed an increasing expression of SPARC protein from normal gastric mucosa (-), to IM (+- to +), and to GC (+ to ++), with significant differences (P < 0.05). Western blot analysis demonstrated significantly higher SPARC expression in induced intestinal cells compared to GES-1. Furthermore, after SPARC knockdown in the human GC cell line HGC27, cell counting kit-8 and colony formation assays showed a reduction in cell proliferative ability, while the wound healing assay revealed impaired cell migration capacity.

CONCLUSION

Comprehensive analysis suggested that a model incorporating clinical tumor node metastasis staging, age, and SPARC/SERPINE1 expression served as a prognostic predictor for GC. Moreover, elevated SPARC expression in IM and GC suggests its potential as a proper biomarker to detect GC in early stage and as a novel therapeutic target, guiding clinical applications.

Identification of CWH43 as a novel prognostic biomarker and therapeutic target in clear cell renal cell carcinoma by a multi-omics approach and correlation with autophagy progression

BACKGROUND

Clear cell renal cell carcinoma (ccRCC) poses significant challenges due to its asymptomatic nature and poor prognosis at advanced stages. Identifying novel biomarkers is essential for enhancing prognostic accuracy and therapeutic strategies. This study explores the CWH43 gene, utilizing multi-omics data to determine its role in ccRCC.

METHODS

Genomic, transcriptomic, and methylation data from TCGA-KIRC and GEO databases were analyzed to evaluate CWH43 expression and clinical impact. Bioinformatics tools assessed correlations with patient outcomes and pathway involvement.

RESULTS

CWH43 expression was significantly reduced in ccRCC tissues and correlated with advanced disease stages and poor patient survival. Enrichment analyses revealed CWH43's involvement in critical cancer pathways, such as autophagy and immune response modulation, suggesting its significant role in ccRCC pathophysiology. Lower CWH43 levels were associated with increased tumor progression and immune evasion, impacting the tumor microenvironment.

CONCLUSION

This study highlights the utility of multi-omics data in identifying CWH43 as a novel prognostic biomarker for ccRCC. Integrating CWH43 into clinical practice could refine prognostic assessments and guide personalized therapy strategies, aligning with advancements in modern oncology. Further research is warranted to explore CWH43's mechanisms and therapeutic potential.

Bypassing the guardian: regulated cell death pathways in p53-mutant cancers

Approximately half of all cancers bear mutations in the tumor suppressor p53. Despite decades of research studying p53 function, treatment of p53-mutant cancers remains challenging owing to the effects of p53 mutations on many complex and interrelated signaling networks that promote tumor metastasis and chemoresistance. Mutations in p53 promote tumor survival by dysregulating cellular homeostasis and preventing activation of regulated cell death (RCD) pathways, which normally promote organismal health by eliminating dysregulated cells. Activation of RCD is a hallmark of effective cancer therapies, and p53-mutant cancers may be particularly susceptible to activation of certain RCD pathways. In this review, we discuss four RCD pathways that are the targets of emerging cancer therapeutics to treat p53-mutant cancers. These RCD pathways include E2F1-dependent apoptosis, necroptosis, mitochondrial permeability transition-driven necrosis, and ferroptosis. We discuss mechanisms of RCD activation, effects of p53 mutation on RCD activation, and current pharmaceutical strategies for RCD activation in p53-mutant cancers.

Unraveling the interrelationship between breast cancer and endometriosis based on multi-omics analysis

BACKGROUND

Endometriosis and breast cancer are significant global health burdens affecting women worldwide. Both conditions share notable characteristics including estrogen dependence, progressive growth patterns, recurrence tendencies, and metastatic potential. Despite these biological parallels, the molecular mechanisms connecting these conditions remain incompletely characterized. This study aimed to identify shared gene signatures and underlying molecular processes in breast cancer and endometriosis.

METHODS

Expression matrices for both conditions were obtained from the Gene Expression Omnibus (GEO), UCSC Xena, and the Molecular Taxonomy of Breast Cancer International Consortium. Common differentially expressed genes (DEGs) were identified using the limma package. Comprehensive analyses included Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, machine learning-based diagnostic and prognostic model development, potential therapeutic compound screening, tumor immune microenvironment (TIME) characterization, and hub gene identification with subsequent validation.

RESULTS

The analysis identified 47 common DEGs between breast cancer and endometriosis. Functional assessment of these genes revealed their involvement in critical biological processes including cell cycle regulation, oxidative stress response, and secretory granule and recycling endosome dynamics. Integration of comprehensive genomic and clinical data led to the development of a prognostic model for breast cancer and a diagnostic model for endometriosis.

CONCLUSION

This study provides molecular insights into shared pathogenic mechanisms underlying breast cancer and endometriosis, highlighting common physiological pathways and key regulatory genes. These findings offer novel perspectives for understanding disease pathogenesis and potential therapeutic interventions for both conditions.

Utilizing cohort-level and individual networks to predict best response in patients with metastatic triple negative breast cancer

Given the highly aggressive and heterogeneous nature of metastatic triple-negative breast cancer, molecular subtypes have been evaluated for their utility in patient stratification and therapeutic selection. Leveraging both our unique longitudinal multimodal analysis of serial tumor biopsies, as well as existing public reference cohorts, we refined clinically relevant molecular subtypes through de-novo network-based approaches. A plasma/B-cell related co-expression module emerged as a robust predictor of clinical response. Refinements of this module were significantly associated with pathological complete response and survival in the CALGB and METABRIC cohorts, as well as dramatically improving the call rate in a CLIA setting. We explored patient-specific networks to monitor individual adaptive responses to therapy, allowing for dynamic adjustments in treatment strategies. Our work supports the shift from traditional molecular subtyping towards a more integrated view that includes the tumor microenvironment and immune landscape in a network-based context.

Molecular patterns and mechanisms of tumorigenesis in HPV-associated and HPV-independent sinonasal squamous cell carcinoma

Mechanisms of tumorigenesis in sinonasal squamous cell carcinoma (SNSCC) remain poorly understood due to its rarity. A subset of SNSCC is associated with human papillomavirus (HPV), but it is unclear whether HPV drives tumorigenesis or acts as a neutral bystander. Here, we show that HPV-associated SNSCC shares mutational patterns found in HPV-associated cervical and head and neck squamous cell carcinoma, including lack of TP53 mutations, hotspot mutations in PI3K and FGFR3, enrichment of APOBEC mutagenesis, viral integration at known hotspots, and frequent epigenetic regulator alterations. We identify HPV-associated SNSCC-specific recurrent mutations in KMT2C, UBXN11, AP3S1, MT-ND4, and MT-ND5, with KMT2D and FGFR3 mutations correlating with reduced overall survival. We establish an HPV-associated SNSCC cell line, showing that combinatorial small-molecule inhibition of YAP/TAZ and PI3K synergistically suppresses clonogenicity. Combining YAP/TAZ blockade with vertical PI3K inhibition may benefit HPV-associated SNSCC, whereas targeting MYC and horizontal inhibition of RAS/PI3K may suit HPV-independent SNSCC.

Epithelial Regnase-1 inhibits colorectal tumor growth by regulating IL-17 signaling via degradation of NFKBIZ mRNA

Regnase-1 is a ribonuclease that regulates inflammation in immune cells by degrading cytokine mRNA. Regnase-1 was identified as one of the frequently mutated genes in the inflamed colorectal epithelium of patients with ulcerative colitis; however, its significance in intestinal epithelial cells during the tumorigenic process remains unknown. Therefore, we developed an ApcMin/+ mouse model lacking Regnase-1 in intestinal epithelia. Regnase-1 deletion significantly enhanced colon tumor growth accompanied by elevated levels of extracellular signal-regulated kinase (ERK) phosphorylation in tumor tissues. Transcriptome analysis of the tumor tissues revealed that Nfkbiz, a mediator of the interleukin (IL)-17 signaling pathway, was the primary degradative target of Regnase-1 in enterocytes and that Regnase-1 deficiency enhanced IL-17 signaling. The treatment with antibiotics or IL-17-neutralizing antibody canceled the proliferative effect of colon tumors due to Regnase-1 deletion, suggesting the protective role of Regnase-1 against colon tumor growth was dependent on IL-17 signaling triggered by gut microbes. Analysis of the Nfkbiz knockout mouse model demonstrated that the tumor-suppressive effect of Regnase-1 depended on Nfkbiz expression. Remarkably, oral treatment of dimethyl fumarate, a potential inhibitor of Regnase-1 protein inactivation, suppressed tumor growth, downregulated Nfkbiz, and suppressed ERK activation. Furthermore, TCGA data analysis revealed that low Regnase-1 expression in colorectal cancer tissue was related to poor prognosis. Therefore, Regnase-1 represses colon tumor growth by regulating IL-17 signaling via Nfkbiz mRNA degradation. Regnase-1 could be a potential therapeutic target in colon tumors.

CT and MRI features of Catenin Beta 1-mutated hepatocellular carcinoma in a Western cohort

OBJECTIVES

Various mutations in hepatocellular carcinoma (HCC) carry prognostic implications. The objective of this study is to assess CT and MRI imaging features associated with Catenin Beta-1 (CTNNB1) mutation in HCC.

METHODS

This retrospective, IRB- approved multi-reader, single-center study included treatment-naive, pathologic-proven HCC that underwent contrast-enhanced CT, MRI or both, with subsequent targeted tumor sequencing test. Preoperative CT and MRI were reviewed for the Liver Imaging Reporting and Data System (LI-RADS, LR) features and prognostic imaging features. Fisher's exact test and multiple testing adjustment were used to assess the association of imaging features and CTNNB1 mutation status.

RESULTS

Of the 160 HCCs included (median age 69 [IQR: 62, 75], 125 men), 58 (36%) had CTNNB1 mutation. Compared to wildtype, CTNNB1-mutated HCCs were more likely to be present as solitary lesion (CT: 26/43[60%] vs. 31/80 [40%], p = 0.024), have mosaic appearance (MRI: 9/34[26%] vs. 3/68[4.4%], p = 0.002), blood products in mass (CT: 7/43[16%] vs. 2/80[2.5%], p = 0.009; MRI: 12/34[35%] vs. 8/68[12%], p = 0.008), necrosis (CT: 16/43[37%] vs. 14/80[18]%, p = 0.026), intralesional arteries (CT: 26/43[60%] vs. 32/80[40%], p = 0.038). A subgroup of 98 high risk patients (hepatitis B, morphologic cirrhosis) were assigned LI-RADS categorization; majority of patients were assigned LR-5 (CT: 15/25[60%] vs. 21/52[40%]; MRI: 10/18[56%] vs. 19/44[43%]). No feature was significantly associated with CTNNB1 mutation status after multiple testing adjustment.

CONCLUSION

Compared to wildtype, CTNNB1-mutated HCCs are more likely to appear as solitary masses with mosaic, heterogeneous appearance containing blood products, necrosis and intralesional arteries. Majority of CTNNB1-mutated tumors were categorized as LR-5 in a subgroup of high risk patients. No imaging feature independently predicted CTNNB1-mutated HCCs.

Small molecule disruption of RARα/NCoR1 interaction inhibits chaperone-mediated autophagy in cancer

Chaperone-mediated autophagy (CMA), a type of selective degradation of cytosolic proteins in lysosomes, is commonly upregulated in cancer cells, contributing to their survival and growth. The lack of a specific target for CMA inhibition has limited CMA blockage to genetic manipulations or global lysosomal function inhibition. Here, using genetic modulation, transcriptional analysis, and functional studies, we demonstrate a regulatory role for the interaction of the retinoic acid receptor alpha (RARα) and its corepressor, the nuclear receptor corepressor 1 (NCoR1), on CMA in non-small cell lung cancer (NSCLC). By targeting the disruption of the NCoR1/RARα complex with a structure-based screening strategy, we identified compound CIM7, a potent and selective CMA inhibitor that has no effect on macroautophagy. CIM7 preferentially inhibits CMA in NSCLC cells over normal cells, reduces tumor growth in NSCLC cells, and demonstrates efficacy in an in vivo xenograft mouse model with no observed toxicity in blood or major tissues. These findings reveal a druggable mechanism for selective CMA inhibition and a first-in-class CMA inhibitor as a potential therapeutic strategy for NSCLC.

Increasing Stemness Drives Prostate Cancer Progression, Plasticity, Therapy Resistance and Poor Patient Survival

Cancer progression involves loss of differentiation and acquisition of stem cell-like traits, broadly referred to as "stemness". Here, we test whether the level of stemness, assessed by a transcriptome-derived Stemness score, can quantitatively track prostate cancer (PCa) development, progression, therapy resistance, metastasis, plasticity, and patient survival. Integrative analysis of transcriptomic data from 87,183 samples across 26 datasets reveals a progressive increase in Stemness and decline in pro-differentiation androgen receptor activity (AR-A) along the PCa continuum, with metastatic castration-resistant PCa (mCRPC) exhibiting the highest Stemness and lowest AR-A. Both the general Stemness score and a newly developed 12-gene "PCa-Stem Signature" correlate with and predict poor clinical outcomes. Mechanistically, increased AR-A may promote Stemness in early-stage PCa while MYC amplification and bi-allelic RB1 loss likely drive greatly elevated Stemness in mCRPC where AR-A is suppressed. Our findings establish Stemness as a robust quantitative measure of PCa aggressiveness and offer a scalable framework for PCa risk stratification.

Genetic landscapes of breast tumors by next-generation sequencing with focus on less common types and genotype-phenotype correlations

Next-generation sequencing (NGS) has transformed our understanding of oncogenic pathways and mutational processes underlying many breast tumors. Although large-scale NGS studies included mostly common invasive breast carcinomas, the genetic landscapes of several less common or rare special histologic types and other breast tumors have now also been elucidated. Many of these lesions harbor highly specific types of mutations or rearrangements/gene fusions, including invasive lobular carcinoma, tall cell carcinoma with reversed polarity, most salivary gland-like neoplasms, fibroepithelial neoplasms, and mesenchymal tumors such as fibromatosis, nodular fasciitis, and dermatofibrosarcoma protuberans. In some cases, surrogate immunohistochemical or RNA in situ hybridization markers evaluable by light microscopy have been shown to correlate with the underlying genetic alterations. Angiosarcomas and other special breast cancer subtypes, such as triple negative apocrine carcinomas, metaplastic carcinomas, and a subset of ER-positive carcinomas (mucinous and micropapillary carcinomas, neuroendocrine neoplasms) have not been associated with specific genetic underpinnings but are enriched for certain genetic features and oncogenic pathways. The identification of characteristic genetic alterations or their molecular surrogates can be useful to establish an accurate diagnosis, and in some cases, may point to potentially actionable therapeutic targets. This review aims to summarize the genetic landscapes of less common benign and malignant breast tumors, with special attention to genotype-phenotype correlations and to the diagnostic utility of genetics and surrogate markers when applicable. BRCA1/2-associated breast carcinomas will also be discussed due to the association of so-called BRCAness with basal-like histology.

Systemic inflammation in response to radiation drives the genesis of an immunosuppressed tumor microenvironment

The composition of the tumor immune microenvironment has become a major determinant of response to therapy, particularly immunotherapy. Clinically, a tumor microenvironment lacking lymphocytes, so-called "cold" tumors, are considered poor candidates for immune checkpoint inhibition. In this review, we describe the diversity of the tumor immune microenvironment in breast cancer and how radiation exposure alters carcinogenesis. We review the development and use of a radiation-genetic mammary chimera model to clarify the mechanism by which radiation acts. Using the chimera model, we demonstrate that systemic inflammation elicited by a low dose of radiation is key to the construction of an immunosuppressive tumor microenvironment, resulting in aggressive, rapidly growing tumors lacking lymphocytes. Our experimental studies inform the non-mutagenic mechanisms by which radiation affects cancer and provide insight into the genesis of cold tumors.

HPV-mediated PARP1 regulation and drug sensitization in head and neck cancer

INTRODUCTION

Human Papillomavirus (HPV)-positive Head and Neck (HNC) cancer responds better to radiotherapy and platinum-based chemotherapy than HPV-negative HNC, likely due to impaired DNA damage repair. Inhibiting PARP1 enhances the effects of radiation and chemotherapy in tumours with defective DNA repair, such as HPV-positive cancers. In this study we investigated the role of HPV in the upregulation of PARP1, determining HNC cell sensitivity to both olaparib and cisplatin.

MATERIALS AND METHODS

PARP1 expression was assessed in HPV-positive and HPV-negative HNC using TCGA data, HNC cell lines and frozen tumour tissue samples from HNC patients. HPV16 expression was modulated by E6/E7 transduction in Human Primary keratinocytes (HK). Sensitivity to the PARP inhibitor olaparib and cisplatin, alone and in combination, was assessed in HNC cell lines.

RESULTS

HPV-positive tumours and cell lines showed upregulated PARP1 expression and activity, mediated by HPV16 oncoproteins. HPV-positive cell lines were more sensitive to olaparib or cisplatin treatment than HPV-negative ones. Combining cisplatin with olaparib synergistically inhibited cell viability in all HNC cell lines tested, regardless of HPV status.

CONCLUSION

Our study demonstrates that PARP1 is upregulated in HPV-positive HN tumours and cell lines, compared to HPV-negative. Despite the higher sensitivity of HPV-positive HNC cell lines to olaparib and cisplatin compared to HPV-negative cells, the combination of cisplatin with olaparib synergistically inhibits cell viability across all HNC cell lines tested, regardless of HPV status. This combination may allow for reduced drug concentrations, potentially decreasing side effects and enhancing therapeutic efficacy in HN tumours.

Prospective study of the real impact of fusion centered genomic assays in patient management in a national collaborative group: the GETHI-XX-16 study

PURPOSE

Precision medicine represents a paradigm shift in oncology. Access to genetic testing and targeted therapies is frequently limited. Assays based on DNA sequencing can miss druggable alterations. We aimed to determine the impact of a free access program to RNA tests in patient management.

METHODS

We designed a multicenter prospective observational study within the Spanish National Group for Translational Oncology and Rare and Orphan Tumors (GETTHI). Eligible patients were adults with solid cancers that had progressed on standard therapies. Tumor samples were analyzed using two RNA sequencing assays (Trailblaze PharosTM and Archer FusionPlex Solid TumorTM). A central committee evaluated the actionability of genetic alterations and reported the findings to attending physicians, who made the final clinical management decisions.

RESULTS

Between November 2016 and April 2019, 395 patients with 41 different tumors across 30 hospitals were included. Molecular analysis revealed actionable genetic alterations in 57 individuals (14.4%). Targeted therapies were advised for 23 and seven received a matched targeted therapy: two lung cancers (EML4-ALK and CD74-ROS1 fusion), three glioblastomas (EGFR point mutations), one oligodendroglioma (FGFR3-TACC3 fusion) and a prostate cancer (SND1-BRAF fusion). The outcomes included two tumor responses, one disease stabilization, one early withdrawal due to toxicity, one progression, and one unknown.

CONCLUSION

Despite the growing knowledge of cancer biology and its translation to drug development, the overall impact of personalized treatments remains low. Access to comprehensive molecular tests covering properly all known actionable alterations and programs for a wide access to targeted therapies seem to be critical steps.

Mitochondrial tRNA fragment, mt-tRF-Tyr-GTA-001 (tRF-21-X3OJI8EWB), in breast cancer and its potential clinical implications

BACKGROUND

Transfer RNA (tRNA) fragments (tRFs) are a group of small non-coding RNAs with biological functions. The involvement of tRNAs in cancer has also been recognized, but most studies focused on nuclear tRFs, very few on mitochondrial tRFs.

METHODS

We analyzed the TCGA microRNAseq data to identify differentially expressed mitochondrial tRFs (mt-tRFs) in breast tumors and evaluated their associations with the disease outcome. Cox proportional hazards regression was used to determine the associations between mt-tRFs and patient survival while adjusting for clinicopathological variables. Quantitative RT-PCR was developed to measure a specific tRF expression in a validation study.

RESULTS

Our analysis of 1,060 tumor samples from TCGA revealed that mt-tRF-Tyr-GTA-001 (tRF-21-X3OJI8EWB or t00018104) expression, a tRF from mitochondrial tRNA with tyrosine anticodon GTA (mt-tRNA-Tyr-GTA), was significantly lower in breast tumors than the adjacent tissues (p< 0.0001). Patients with low expression had significantly higher risk of death (HR = 1.69, p = 0.0018) regardless of their age at diagnosis, disease stage, tumor grade, and hormone receptor status. This survival association was replicated in an independent study where mt-tRF-Tyr-GTA-001 expression was measured with qRT-PCR. Further analysis suggested that the mt-tRF expression was correlated with ribonuclease ANG and RNase 4 known to cleave tRNAs and upregulated under hypoxia. IPA interrogation of the mt-tRF-Tyr-GTA-001 expression signature indicated the inhibitory effects of mt-tRF-Tyr-GTA-001 on malignant transformation, tumor growth, and cell invasion. In silico analysis showed that the binding targets of mt-tRF-Tyr-GTA-001 included several oncogenic transcription factors (E2Fs, CCNE1, FOXM1). We also found the mt-tRF correlated with the abundances of M0 macrophages and resting mast cells, two of the immune cells known for innate immunity.

CONCLUSIONS

In summary, our study suggests that mt-tRF-Tyr-GTA-001, a mitochondrial tRF, may suppress breast cancer progression through its involvement in regulation of cell phenotype and tumor immunity.

TRanscriptome ANalysis of StratifiEd CohorTs (TRANSECT) enables automated assessment of global gene regulation linked to disparate expression in user defined genes and gene sets

Publicly accessible expression data produced by large consortium projects like TCGA and GTEx are increasing in number and size at an unprecedented rate. Their utility cannot be underestimated given the diversity of valuable tools widely used to interrogate these data and the many discoveries of biological and clinical significance already garnered from these datasets. However, there remain undiscovered ways to mine these rich resources and a continuing need to provide researchers with easily accessible and user-friendly applications for complex or bespoke analyses. We introduce TRanscriptome ANalysis of StratifiEd CohorTs (TRANSECT), a bioinformatics application automating the stratification and subsequent differential expression analysis of cohort data to provide further insights into gene regulation. TRANSECT works by defining two groups within a cohort based on disparate expression of a gene or a gene set and subsequently compares the groups for differences in global expression. Akin to reverse genetics minus the inherent requirement of in vitro or in vivo perturbations, cell lines or model organisms and all the while working within natural physiological limits of expression, TRANSECT compiles information about global transcriptomic change and functional outcomes. TRANSECT is freely available as a command line application or online at https://transect.au.

PARP inhibitor response is enhanced in prostate cancer when XRCC1 expression is reduced

Prostate cancer (PCa) is the second most common cancer worldwide and the fifth leading cause of cancer-related deaths among men. The emergence of metastatic castration-resistant prostate cancer (mCRPC) after androgen deprivation therapy (ADT) exemplifies the complex disease management for PCa. PARP inhibitors (PARPis) are being tested to treat mCRPC in tumors with defective homologous recombination repair (HRR) to address this complexity. However, increasing resistance towards PARPi in HRR-deficient patients and the low percentage of HRR-defective mCRPC patients requires the identification of new genes whose deficiency can be exploited for PARPi treatment. XRCC1 is a DNA repair protein critical in the base excision repair (BER) and single strand break repair (SSBR) pathways. We analyzed PCa patients' cohorts and found that XRCC1 expression varies widely, with many patients showing low XRCC1 expression. We created XRCC1 deficiency in PCa models to examine PARPi sensitivity. XRCC1 loss conferred hypersensitivity to PARPi by promoting the accumulation of DNA double-strand breaks, increasing cell-cycle arrest, and inducing apoptosis. We confirmed that XRCC1 expression correlated with PARPi sensitivity using a doxycycline-inducible system. Therefore, we conclude that XRCC1 expression level predicts response to PARPi, and the clinical utility of PARPi in PCa can extend to low XRCC1 expressing tumors.

Characterizing the molecular and spatial heterogeneity of midline gliomas in adults: a single institution analysis

PURPOSE

Primary gliomas arising within midline structures of the central nervous system are associated with a worse prognosis compared with hemispheric gliomas. In adults, compared to their pediatric counterparts, adult midline gliomas are not as clearly characterized on the clinical behavior, prognostic factors, and treatment approaches for these diseases.

METHODS

This retrospective cohort assessed all adult (≥ 18 years) patients from our institution with diffuse gliomas arising from midline structures at time of diagnosis (2014-2020). Molecular features characterized using immunohistochemistry, targeted next-generation sequencing, and chromosomal microarray analysis were collected. Patient characteristics were compared across groups using analysis of variance, Kruskal-Wallis, and the chi-square test as appropriate. Cumulative progression-free survival (PFS) and overall survival (OS) probabilities were estimated using the Kaplan-Meier method. Comparisons across groups were made using the log rank test.

RESULTS

79 patients were included in analysis, with a median follow-up of 22.5 months (range, 0.6-123). The mean age at diagnosis was 44.5 years (range, 19.4-76.4), and 51% (n = 40) were female. Thalamus/basal ganglia was the most common primary tumor location (47%), followed by the brainstem (30%), and cerebellum (23%). For the entire cohort, median PFS was 11.5 months (95% CI 9.4-20.1), and median OS was 25.5 months (95% CI 22.0-38.2). We grouped primary tumor types into four distinct diagnostic entities based on integrated histological and molecular features, which had survival differences (log-rank p = 0.007)-diffuse midline glioma, H3 K27-altered (17% with median OS 19.4 months); astrocytoma, IDH-wild type, not otherwise specified (42% with median OS 25.5 months); glioblastoma, IDH-wild type (24% with median OS 11.0 months); and astrocytoma, IDH-mutant (18% with OS 63.3 months). There were no cases of IDH-mutant tumors in the thalamus/basal ganglia. IDH-mutant tumors had better prognosis (OS: IDH-mutant 63.3 months, IDH-wild type 22.5 months, log-rank p = 0.003). Tumor enhancement and diffusion restriction at initial diagnosis was associated with worse prognosis (OS: enhancing 22.0 months, non-enhancing 64.5 months, log-rank p < 0.001; OS: restriction 20.3 months, no restriction 30.6 months, log-rank p = 0.028).

CONCLUSION

There is significant molecular heterogeneity between midline gliomas which has prognostic implications. These findings emphasize the need to molecularly characterize these tumors to facilitate personalized treatment approaches.

KDM4C inhibition blocks tumor growth in basal breast cancer by promoting cathepsin L-mediated histone H3 cleavage

Basal breast cancer is a subtype with a poor prognosis in need of more effective therapeutic approaches. Here we describe a unique role for the KDM4C histone lysine demethylase in KDM4C-amplified basal breast cancers, where KDM4C inhibition reshapes chromatin and transcriptomic landscapes without substantial alterations of its canonical substrates, trimethylated histone H3 lysine 9 (H3K9me3) and lysine 36 (H3K36me3). Rather, KDM4C loss causes proteolytic cleavage of histone H3 mediated by cathepsin L (CTSL), resulting in decreased glutamate-cysteine ligase expression and increased reactive oxygen species. CTSL is recruited to the chromatin by the grainyhead-like 2 (GRHL2) transcription factor that is methylated at lysine 453 following KDM4C inhibition, triggering CTSL histone clipping activity. Deletion of CTSL rescued KDM4-loss-mediated tumor suppression. Our study reveals a function for KDM4C that connects cellular redox regulation and chromatin remodeling.

Genomic Landscape of Adenocarcinomas Across the Gastroesophageal Junction: Moving on From the Siewert Classification

OBJECTIVE

To investigate how the Siewert classification of gastroesophageal junction adenocarcinomas correlates with genomic profiles.

BACKGROUND

Current staging and treatment guidelines recommend that tumors with an epicenter <2 cm into the gastric cardia be treated as esophageal cancers, whereas tumors with an epicenter >2 cm into the cardia be staged and treated as gastric cancers. To date, however, few studies have compared the genomic profiles of the 3 Siewert classification groups to validate this distinction.

METHODS

Using targeted tumor sequencing data on patients with adenocarcinoma of the gastroesophageal junction previously treated with surgery at our institution, we compared genomic features across Siewert classification groups.

RESULTS

A total of 350 patients were included: 121 had Siewert type I, 170 type II, and 59 type III. Comparisons by Siewert location revealed that Siewert types I and II were primarily characterized as the chromosomal instability molecular subtype and displayed Barrett metaplasia and p53 and cell cycle pathway dysregulation. Siewert type III tumors, by contrast, were more heterogeneous, including higher proportions of microsatellite instability and genomically stable tumors, and more frequently displayed ARID1A and somatic CDH1 alterations, signet ring cell features, and poor differentiation. Overall, Siewert type I and II tumors demonstrated greater genomic overlap with lower esophageal tumors, whereas Siewert type III tumors shared genomic features with gastric tumors.

CONCLUSIONS

Overall, our results support recent updates in treatment and staging guidelines. Ultimately, however, molecular rather than anatomic classification may prove more valuable in determining staging, treatment, and prognosis.

Induction of SOX17 with stimulation of WNT, TGF-beta, and FGF signaling drives embryonal carcinomas into the yolk-sac tumor lineage resulting in increased cisplatin resistance

Relapsing germ cell tumor (GCT) patients often harbor components of the aggressive subtype yolk-sac tumor (YST), suggesting that YST formation is an escape mechanism under therapy. Nevertheless, the molecular mechanisms inducing YST development from its stem cell-like precursor embryonal carcinoma (EC) are largely unexplored. We demonstrated that the induction of the transcription factor SOX17 together with the stimulation of WNT, TGF-beta / Activin, and FGF signaling drives EC cells into the YST lineage. Single cell RNA sequencing revealed that this cell fate switch was accompanied by the upregulation of the typical YST factors AFP, ANKRD1, APOA1, CST1, FOXA2, GATA6, and GPC3 and microRNAs, while pluripotency-related genes NANOG, POU5F1, and SOX2 were downregulated. Chromatin immunoprecipitation followed by sequencing analysis revealed that SOX17 may act in concert with FOXA2 and GATA factors to initiate YST formation. Xenografting of the YST-like cells into nude mice led to the growth of mixed GCT with YST components, confirming that these cells are able to form a YST in vivo. Moreover, the expression of cisplatin resistance factors was induced in a subpopulation of YST-like cells, suggesting that the formation of a YST is accompanied by the acquisition of cisplatin resistance. Indeed, the YST-like cells presented as less sensitive to cisplatin than their parental cells. Our study deciphered the molecular mechanisms forcing EC to differentiate into the YST lineage, which is accompanied by the acquisition of cisplatin resistance, confirming that YST formation is an escape mechanism for GCT under therapy. Thus, GCT patients should be screened for YST elements under therapy to identify patients at risk of developing therapy resistance.

BCL2 drives castration resistance in castration-sensitive prostate cancer by orchestrating reciprocal crosstalk between oncogenic pathways

Progression following androgen-deprivation therapy (ADT) and the development of castration resistance is the leading cause of death among prostate cancer patients. Since there is currently a lack of known driver alterations associated with ADT resistance in castration-sensitive prostate cancer (CSPC), we investigated the critical role of crosstalk between cell signaling networks in early castration resistance. Our preclinical experiments and analyses of RNA sequencing data from clinical trials revealed nearly universal upregulation of BCL2 after ADT in CSPC cells. Mechanistically, our findings highlight a non-canonical function of BCL2 in orchestrating reciprocal signaling between the androgen receptor (AR)-BCL2 and phosphatidylinositol 3-kinase (PI3K) pathways, particularly upon ADT, potentially driving CSPC transformation into lethal castration-resistant prostate cancer (CRPC). Critically, our results provide a scientific rational that BCL2 inhibition should be trialed in CSPC in combination with ADT to impede or delay ADT-induced CSPC-to-CRPC transformation but may be ineffective if tested in patients who already have CRPC.

SLIT/ROBO Pathway and Prostate Cancer: Gene and Protein Expression and Their Prognostic Values

Prostate cancer (PCa) is the second most common cancer and the second leading cause of cancer-related mortality among men. Gene expression analysis has been crucial in understanding tumor biology and providing disease progression markers. Cell surface glycoproteins and those in the extracellular matrix play significant roles in the PCa microenvironment by promoting migration, invasion, and metastasis. The molecular and histopathological heterogeneity of prostate tumors necessitates a new marker discovery to better stratify patients at risk for poor prognosis. In this study, our objectives were to investigate and characterize the localization and expression of SLIT/ROBO in PCa samples from transgenic mice and human tumor samples, aiming to identify novel prognostic markers and potential therapeutic targets. We conducted histopathological, immunohistochemical, and bioinformatics analyses on prostate tumors from two knockout mice models (Pb-Cre4/Ptenf/f and Pb-Cre4/Trp53f/f;Rb1f/f) and human prostate tumors. Transcriptomic analyses revealed special changes in the expression of genes related to the SLIT/ROBO neural signaling pathway. We further characterized the gene and protein expression of the SLIT/ROBO pathway in knockout animal samples, and protein expression in the PCa samples of patients with different Gleason scores. Public datasets with clinical data from patients (The Human Protein Atlas, cBioPortal, SurvExpress and CamcAPP) were used to validate the gene and protein expression of SLIT1, SLIT2, ROBO1, and ROBO4, correlating these alterations with the prognosis of subgroups of patients. Our findings highlight potential biomarkers of the SLIT/ROBO pathway with prognostic and predictive value, as well as promising therapeutic targets for PCa.

FOXA2 promotes metastatic competence in small cell lung cancer

Small cell lung cancer (SCLC) is known for its high metastatic potential, with most patients demonstrating clinically evident metastases in multiple organs at diagnosis. The factors contributing to this exceptional metastatic capacity have not been defined. To bridge this gap, we compare gene expression in SCLC patient samples who never experienced metastasis or relapse throughout their clinical course, versus primary SCLC patient samples from more typical patients who had metastatic disease at diagnosis. This analysis identifies FOXA2 as a transcription factor strongly associated with SCLC metastasis. Subsequent analyses in experimental models demonstrates that FOXA2 induces a fetal neuroendocrine gene expression program and promotes multi-site metastasis. Moreover, we identify ASCL1, a transcription factor known for its initiating role in SCLC tumorigenesis, as a direct binder of the FOXA2 promoter and regulator of FOXA2 expression. Taken together, these data define the ASCL1-FOXA2 axis as a critical driver of multiorgan SCLC metastasis.

Unveiling the multifaceted functions of TRIM proteins in glioma pathogenesis

Gliomas, the most prevalent malignant primary brain tumors in adults, represent a heterogeneous group of neoplasms characterized by poor prognosis and limited therapeutic options, particularly in high-grade cases. Understanding the molecular mechanisms underlying glioma pathogenesis is crucial for developing novel and effective treatment strategies. In recent years, increasing attention has been directed toward the tripartite motif (TRIM) family of proteins, a class of E3 ubiquitin ligases, due to their significant roles in glioma development and progression. This review comprehensively explores the diverse functions of TRIM proteins in gliomas, including their expression patterns, prognostic significance, and mechanisms of action that are both ubiquitination-dependent and -independent. By synthesizing current knowledge, we aim to elucidate the role of TRIM proteins in glioma pathogenesis and identify potential therapeutic targets within this protein family.

COPS4 is a novel prognostic biomarker and potential therapeutic target involved in regulation of immune microenvironment in numerous cancers

CHOL, HNSC, ESCA, and LIHC are among the most aggressive and fatal malignancies worldwide. Despite their clinical burden, these cancers still lack dependable biomarkers for early detection, prognosis, and therapeutic targeting. The COP9 signalosome (COPS), a key regulator of the ubiquitin proteasome pathway, has been shown to be aberrantly expressed in various cancer types and is thought to contribute to tumor development and progression. Among its subunits, COPS4 plays an essential role in maintaining the functional integrity of the complex. However, its prognostic significance and clinicopathological relevance in cancer remain poorly understood. This study adopted a comprehensive, integrative bioinformatics framework grounded in TCGA-derived datasets, incorporating analytical platforms encompassing UALCAN, GEPIA, MEXPRESS, OncoDB, UCSC Xena, ENCORI, TIMER, GeneMANIA, TNMplot, and TISIDB. Through this strategy, the investigation delineated the transcriptional landscape, genomic aberrations, immunological associations, and putative functional roles of COPS4 across CHOL, HNSC, ESCA, and LIHC. Virtual screening and molecular dynamics simulations were performed to explore its druggable potential. COPS4 expression was significantly upregulated in tumor tissues and exhibited strong associations with key clinical parameters, including pathological stage, histological grade, nodal involvement, and metastatic status. IHC analysis further validated elevated protein levels in tumor specimens compared to adjacent non-neoplastic tissues. Genomic alterations were frequent, with predominant mutations in LIHC, amplifications in CHOL, and both amplifications and deletions in HNSC and ESCA. COPS4 expression showed positive associations with subset of oncogenes and inverse correlations with tumor suppressors. Notably, NUP54 and HELQ emerged as consistent co-targets. Immune analysis revealed strong positive correlations between COPS4 and infiltrating immune cells, including CD8+ and CD4+ T cells, B cells, macrophages, neutrophils, and dendritic cells. Somatic copy number variations of COPS4 also influenced immune cell infiltration and patient survival outcomes. Promoter hypomethylation and gene amplification were identified as mechanisms driving its overexpression. Finally, virtual screening and molecular dynamics simulations identified FDA-approved drugs interacting with COPS4, emphasizing its oncogenic role and therapeutic potential.

Integrative Analysis of EPHX4 as a Novel Prognostic and Diagnostic Biomarker in Lung Adenocarcinoma

Lung adenocarcinoma (LUAD) remains a leading cause of cancer-related mortality, necessitating the identification of novel biomarkers for improved prognosis and diagnosis. This study investigates the role of epoxide hydrolase 4 (EPHX4), a member of the epoxide hydrolase family, in LUAD. Using data sourced from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) databases, which were subsequently validated by the Gene Expression Omnibus (GEO), we analyzed levels of EPHX4 expression, mutation, and methylation in tumors versus normal tissues. Our findings revealed a significant upregulation of EPHX4 in LUAD tissues compared to normal lung tissues (p < 0.001), correlating with poorer overall survival (OS), disease-specific survival (DSS), and progression-free interval (PFI). Furthermore, EPHX4 exhibited considerable diagnostic potential, as demonstrated by an area under the curve (AUC) of 0.854 in a Receiver Operating Characteristic (ROC) analysis. Notably, EPHX4 expression was associated with immune infiltration, specifically Th2 cells, neutrophils, and macrophages, along with immune checkpoint molecules including PD-L1, PD-L2, and TIM-3. Additionally, EPHX4 was involved in pivotal tumor-associated pathways, particularly cell cycle regulation. In conclusion, an elevated EPHX4 expression is indicative of poorer prognosis in LUAD and may play a role in immune evasion and cell cycle dysregulation, highlighting its potential as a promising biomarker for the diagnosis and prognostic prediction of LUAD.

PIWIL2 downregulation in colon cancer promotes transposon activity and pro-tumorigenic phenotypes

Reactivation of transposable elements (TEs) in somatic tissues, particularly of LINE-1, is associated with disease by causing gene mutations and DNA damage. Previous work has shown that the PIWI pathway is crucial for TE suppression in the germline. However, the status and function of this pathway has not been well characterized in differentiated somatic cells and there is lack of consensus on the role of the pathway in somatic tumorigenesis. To shed light on this conundrum, we examined the PIWI pathway in colon cancer through a combination of bioinformatic analyses and cell-based assays. Shifted Weighted Annotation Network (SWAN) analysis revealed that the pathway experiences significant allelic losses in colon cancer and that PIWIL2, the main catalytic component of the pathway responsible for TE silencing, experiences the highest percent deletions. PIWIL2 is downregulated in colon tumors of advanced stage, nodal metastasis, and in certain subtypes, correlating with poor survival, while it is even downregulated in ulcerative colitis, an inflammatory bowel disease that predisposes to colon cancer. Knockout studies in colon epithelial Caco2 cells show that PIWIL2 depletion leads to increased anchorage-independent growth, increased LINE-1 levels and activity, and in DNA damage, altogether highlighting a tumor-suppressing role of PIWIL2 in the colon.

Combined analysis of somatic mutations and gene expression reveals nuclear speckles-associated enhanced stemness in gingivobuccal carcinoma under DNA damage response

Smokeless tobacco chewing habits in India lead to a high prevalence of Gingivobuccal oral squamous cell carcinoma (OSCC-GB). Cancer stem cells (CSCs) are a sub-population of cancer cells within a tumor with stem-like properties and are believed to contribute to tumor initiation, progression, increased resistance to drug therapy, and promote post-therapeutic cancer relapse. An RNA-sequencing data-based combined analysis of somatic mutations and gene expression was performed to explore the role of CSCs in disease progression using the novel Indian-origin OSCC-GB cell line 'IIOC019' from a patient with tobacco-chewing habit. The identified DNA damage-related known mutational signature (1 bp T/(A) nucleotide insertions and C>T mutations) indicates the impact of smokeless tobacco-related carcinogens in the IIOC019 cell line. The differentially expressed somatic variants, functional impact predictions, and survival analysis reveal the role of DNA damage response (DDR)-related genes in OSCC-GB, with the SON gene as a significant player. The study suggests that the loss-of-function in a somatic variant of the SON gene is linked to nuclear speckles-associated enhanced stemness and increased risk of disease progression in OSCC-GB under DDR conditions. The newly identified CSC-associated somatic variants appear to promote cancer spread, local recurrence, and resistance to chemotherapy or radiotherapy, contributing to the high mortality rates among Indian OSCC-GB patients.

Integration of cuproptosis-related gene signatures in stomach adenocarcinoma: implications for prognostic prediction and therapeutic strategies in cancer drug resistance

BACKGROUND

Stomach adenocarcinoma (STAD) is a prevalent and aggressive cancer, often diagnosed at later stages, which poses challenges for effective treatment. Despite advancements in cancer therapies, the phenomenon of tumor drug resistance remains a critical hurdle. Recent studies have highlighted cuproptosis, a copper-dependent regulated cell death process, as a potential mechanism in various cancers, including STAD. This study integrates cuproptosis-related gene signatures with clinical features to better predict prognosis and explore potential therapeutic targets, focusing on the role of cuproptosis in overcoming tumor resistance mechanisms.

METHODS

Using comprehensive datasets from TCGA-STAD (n = 375 tumor samples, 32 normal samples), GTEx (n = 211 normal gastric tissues), and GEO (GSE84437 and GSE29272), we analyzed the expression of genes associated with cuproptosis. We examined genetic alterations, immune infiltration, and constructed multivariate Cox regression models with clinicopathological covariates (age, gender, TNM stage, histological grade, residual tumor status) to assess the relationship between cuproptosis gene expression and patient survival outcomes, including overall survival (OS), disease-specific survival (DSS), and progression-free interval (PFI). Drug sensitivity analysis was performed using the Genomics of Drug Sensitivity in Cancer (GDSC) database.

RESULTS

Our analysis identified significant upregulation of several cuproptosis-related genes, including FDX1, which was correlated with improved prognosis and immune cell infiltration patterns. High expression of FDX1 was associated with better OS and DSS outcomes. Further genetic alterations, notably in CDKN2A, were frequent and linked to poor prognosis, highlighting the complexity of tumor drug resistance in STAD. Prognostic models incorporating FDX1, PDHA1, and LIAS expression stratified patients into distinct risk categories, emphasizing their potential as biomarkers for personalized therapeutic strategies.

CONCLUSIONS

This study underscores the importance of cuproptosis-related genes, particularly FDX1, in the prognosis and therapeutic response of STAD. By integrating molecular features with clinical data, we offer insights into the potential for overcoming drug resistance in cancer therapy. These findings lay the groundwork for future research into targeted treatments that modulate cuproptosis, offering a novel approach to tackling tumor progression and resistance in STAD.

An Intrinsically Disordered Region of the FACT Subunit, Spt16, Promotes Chromatin Disassembly in Stimulating the Pre-Initiation Complex Formation at the Promoter for Transcription Initiation In Vivo

Previous structural and biochemical studies revealed that a negatively charged intrinsically disordered region (IDR) at the C-terminal of the Spt16 subunit of an evolutionarily conserved heterodimeric histone chaperone, FACT (Facilitates chromatin transcription), interacts with histone H2A-H2B dimer, and hence interferes the interaction of DNA with histone H2A-H2B dimer. However, the functional relevance of the binding of Spt16's IDR to histone H2A-H2B dimer with impact on chromatin dynamics and transcription has not been clearly elucidated in living cells. Here, we show that Spt16's IDR facilitates the eviction of histone H2A-H2B dimer (and hence chromatin disassembly) from the inducible GAL promoters upon transcription induction. Such facilitation of chromatin disassembly by Spt16's IDR stimulates the pre-initiation complex (PIC) formation at the promoter, and hence transcription initiation. Further, we find that Spt16's IDR regulates chromatin reassembly at the coding sequence in the wake of elongating RNA polymerase II. Collectively, our results reveal that Spt16's IDR facilitates promoter chromatin disassembly for stimulation of the PIC formation for transcription initiation with additional function in chromatin reassembly at the coding sequence in the wake of elongating RNA polymerase II, thus illuminating novel IDR regulation of chromatin dynamics and transcription in vivo.

LMTK3 regulation of EV biogenesis and cargo sorting promotes tumour growth by reducing monocyte infiltration and driving pro-tumourigenic macrophage polarisation in breast cancer

BACKGROUND

Lemur Tail Kinase 3 (LMTK3) promotes cell proliferation, invasiveness and therapy resistance, and its expression correlates with poor survival in several different malignancies, including breast cancer. Crosstalk through extracellular vesicles (EVs) is an increasingly appreciated mechanism of cell communication within the tumour immune microenvironment, which contributes to different aspects of cancer progression and plays a pivotal role in shaping tumour fate.

METHODS

Nanoparticle tracking analysis and transmission electron microscopy were used to study the effects of LMTK3 on EV size, while single particle interferometry allowed us to examine LMTK3-dependent effects on the subpopulation distribution of EVs. Quantitative mass spectrometry was used to profile LMTK3-dependent proteomics changes in breast cancer-derived EVs. Bioinformatics analysis of clinical data along with in vitro and cell-based assays were implemented to explore the effects of LMTK3-dependent EV protein cargo on the tumour immune microenvironment. To elucidate the mechanism through which LMTK3 impacts endosomal trafficking and regulates EV biogenesis, we used a variety of approaches, including in vitro kinase assays, confocal and electron microscopy, as well as in vivo subcutaneous and orthotopic breast cancer mouse models.

RESULTS

Here, we report that LMTK3 increases the average size of EVs, modulates immunoregulatory EV proteomic cargo and alters the subpopulation distribution of EVs released by breast cancer cells. Mechanistically, we provide evidence that LMTK3 phosphorylates Rab7, a key regulator of multivesicular body (MVB) trafficking, thereby reducing the fusion of MVBs with lysosomes and subsequent degradation of intralumenal vesicles, resulting in altered EV release. Moreover, LMTK3 causes increased packaging of phosphoserine aminotransferase 1 (PSAT1) in EVs, leading to a paracrine upregulation of phosphoglycerate dehydrogenase (PHGDH) in monocytes when these EVs are taken up. PSAT1 and PHGDH play key roles in the serine biosynthesis pathway, which is closely linked to cancer progression and regulation of monocyte behaviour. LMTK3 EV-induced elevated PHGDH expression in monocytes reduces their infiltration into breast cancer 3D spheroids and in vivo breast cancer mouse models. Furthermore, these infiltrating monocytes preferentially differentiate into pro-tumourigenic M2-like macrophages. Additional breast cancer mouse studies highlight the contribution of LMTK3-dependent EVs in the observed immunosuppressive macrophage phenotype. Finally, in vitro experiments show that pharmacological inhibition of LMTK3 reverses the pro-tumourigenic and immunomodulatory effects mediated by EVs derived from LMTK3 overexpressing cells.

CONCLUSION

Overall, this study advances our knowledge on the mechanisms of EV biogenesis and highlights a novel oncogenic role of LMTK3 in the breast TME, further supporting it as a target for cancer therapy.

Iterative refinement and goal articulation to optimize large language models for clinical information extraction

Extracting structured data from free-text medical records at scale is laborious, and traditional approaches struggle in complex clinical domains. We present a novel, end-to-end pipeline leveraging large language models (LLMs) for highly accurate information extraction and normalization from unstructured pathology reports, focusing initially on kidney tumors. Our innovation combines flexible prompt templates, the direct production of analysis-ready tabular data, and a rigorous, human-in-the-loop iterative refinement process guided by a comprehensive error ontology. Applying the finalized pipeline to 2297 kidney tumor reports with pre-existing templated data available for validation yielded a macro-averaged F1 of 0.99 for six kidney tumor subtypes and 0.97 for detecting kidney metastasis. We further demonstrate flexibility with multiple LLM backbones and adaptability to new domains, utilizing publicly available breast and prostate cancer reports. Beyond performance metrics or pipeline specifics, we emphasize the critical importance of task definition, interdisciplinary collaboration, and complexity management in LLM-based clinical workflows.

Differential gene set enrichment of the epithelial-mesenchymal transition pathway in BRAF- vs. NRAS-mutated metastatic melanoma

Melanoma is a leading cause of cancer-related deaths and is frequently driven by mutations in the BRAF and NRAS genes. These mutations disrupt key cellular signalling pathways that promote tumour growth and metastasis, but they have distinct biological and clinical implications, particularly in their response to treatment and impact on patient prognosis. The epithelial-mesenchymal transition (EMT) is a process in which epithelial cells undergo changes in response to specific transcription factors. There are currently few studies investigating the EMT within BRAF and NRAS mutations. The aim of this study was to further elucidate activation of the EMT pathway in metastatic melanoma, focusing on BRAF- and NRAS-mutated samples from The Cancer Genome Atlas. Gene Set Enrichment Analysis revealed that BRAF mutations were more significantly associated with increased EMT activation relative to all other mutations in the dataset. In contrast, NRAS mutations were not significantly associated with gene expression of the EMT pathway, suggesting alternative mechanisms for metastasis.

RAP1GAP is a prognostic biomarker and correlates with immune infiltrates in bladder cancer

BACKGROUND

The role of RAP1GAP in tumor progression has garnered increasing attention; however, its prognostic value and immunological influence across various cancers remain uncertain. Our study presents a pan-cancer analysis to investigate its involvement in oncogenesis and immune regulation.

METHODS

Public databases were utilized to assess RAP1GAP expression across cancers. Cox regression analysis evaluated its prognostic value, while Pearson correlation examined associations with genomic heterogeneity, tumor stemness, immune cell infiltration, and immune checkpoints. Immunohistochemical staining of bladder cancer and adjacent tissues assessed RAP1GAP expression and clinical correlations.

RESULTS

RAP1GAP expression is differentially expressed in a variety of tumor types and predicts a better or worse prognosis for tumor patients. It was strongly linked to genomic heterogeneity and tumor stemness in multiple cancers. Immunohistochemistry showed increased RAP1GAP expression in bladder cancer. Immune cell analysis revealed high RAP1GAP expression was associated with greater infiltration of plasma cells, naive CD4 + T cells, Tregs, and eosinophils, while low expression correlated with increased CD8 + T cells, activated memory CD4 + T cells, and M1 macrophages.

CONCLUSION

RAP1GAP is a potential prognostic biomarker and immune regulator, with promising implications as an immunotherapeutic target for bladder cancer.

HDAC6 facilitates LUAD progression by inducing EMT and enhancing macrophage polarization towards the M2 phenotype

Histone deacetylase 6 (HDAC6) plays a critical role in lung adenocarcinoma (LUAD) prognosis and the tumor immune microenvironment (TIME). This study, utilizing public datasets and experimental validation, revealed that HDAC6 is upregulated in LUAD, correlating with poor survival outcomes and an immunosuppressive TIME characterized by increased Tregs, CAFs, M2 macrophages, and MDSCs. HDAC6-high patients showed reduced immunotherapy response. HDAC6 knockout inhibited tumor growth, suppressed PI3K/AKT/mTOR signaling and EMT, and enhanced apoptosis and M1 macrophage recruitment. HDAC6 inhibition synergized with anti-PD-1 therapy, suggesting a potential combinatorial strategy for LUAD treatment. HDAC6 serves as a key prognostic marker and therapeutic target in LUAD.

Multidimensional investigation of thyroid hormones and prostate cancer: insights from NHANES, Mendelian randomization, genetic markers, and bioinformatics analyses

BACKGROUND

Prostate cancer remains a major global health burden for men, with its incidence and mortality steadily rising. Thyroid hormones, critical regulators of metabolism and cell growth, have been implicated in tumorigenesis, yet their specific role in prostate cancer risk remains unclear. This study systematically investigates the relationship between thyroid hormones and prostate cancer using multidimensional approaches.

METHODS

A three-phase study design was employed: (1) A cross-sectional analysis of The National Health and Nutrition Examination Survey (NHANES) data to examine thyroid hormone levels (FT3 and T3) and prostate cancer risk; (2) Mendelian randomization (MR) analysis using genome-wide association studies (GWAS) data to explore causal relationships; (3) Bioinformatics analyses to annotate key Single Nucleotide Polymorphism(SNPs), identify related genes, and assess their biological roles in prostate cancer.

RESULTS

Observational analysis revealed significantly lower FT3 and T3 levels in high-risk prostate cancer patients, with adjusted models confirming an inverse association (p < 0.001). MR analysis supported a causal relationship between thyroid hormone replacement therapy and reduced prostate cancer risk (b < 0, p < 0.05). Four key genes-ADM5, INPP5B, NEURL4, and TYK2-were identified as downregulated in prostate cancer tissues, with prognostic and immune regulatory implications.

CONCLUSIONS

Thyroid hormones exhibit a protective role against prostate cancer. ADM5, INPP5B, NEURL4, and TYK2 emerge as potential biomarkers and therapeutic targets, warranting further mechanistic and clinical validation.

The Molecular Motor Myosin 5B and Its Folding Chaperone UNC45A Are Decreased in Colorectal Cancer

BACKGROUND & AIMS

Colorectal cancer (CRC) ranks among the most common and deadliest cancers worldwide. Previous studies have found that the molecular motor Mysoin 5b (MYO5B) is decreased at the level of mRNA in CRC, but the mechanism behind this reduction remains unknown. In normal cells, MYO5B function is contingent on proper folding by the chaperone protein unc-45 myosin chaperone A (UNC45A). However, little is known about the role of UNC45A in CRC.

METHODS

We examined RNA, methylation, and protein levels of MYO5B and UNC45A and identified microRNAs (miRNAs) targeting UNC45A in normal colon, colon adenocarcinoma (COAD) samples, cancer cell lines, and human colonic organoids. Cells were treated with the DNA-demethylating agent 5-aza-2'-deoxycytidine to examine the role of methylation in regulating MYO5B levels. Additionally, the UNC45A targeting miR-296-3p was inhibited in cells, and UNC45A levels were examined.

RESULTS

Consistent with previous reports, we found that MYO5B mRNA was reduced in COAD compared with controls. We observed that the MYO5B gene was hyper-methylated in COAD and treatment of cancer cells with a demethylating compound increased MYO5B expression, suggesting that methylation silences MYO5B in COAD. The MYO5B folding chaperone UNC45A was not changed at the mRNA level but was decreased at the protein level. We identified several UNC45A targeting miRNAs that were elevated in COAD patients. We confirmed that these miRNAs were elevated in colon cancer cell lines compared with normal colonic organoids and found that inhibition of one of these miRNAs increased UNC45A protein.

CONCLUSIONS

These findings suggest that decreased levels of MYO5B in COAD may result from gene methylation and improper folding by UNC45A.

Pan-cancer oncogenic properties and therapeutic potential of SF3B4

Splicing factor 3B (SF3B) subunit 4 (SF3B4), an SF3B complex component essential for spliceosome assembly and accurate splicing, plays a major role in cancer development. However, the precise mechanism through which SF3B4 contributes to tumor growth remains unclear. Here, we demonstrate that SF3B4 is strongly expressed in patients with various cancer types and correlated with their survival. By using hepatocellular carcinoma (HCC) as a model, we reveal that SF3B4's interactions with and regulatory influence on the checkpoint protein BUB1 are essential for appropriate cancer cell mitosis and proliferation. Our results thus demonstrate the roles of SF3B4 as both a cell-cycle regulator and an oncogenic factor in HCC, highlighting its potential as a pan-cancer therapeutic target and diagnostic biomarker.

Dissecting the immune landscape in pediatric high-grade glioma reveals cell state changes under therapeutic pressure

Pediatric high-grade gliomas (pHGGs) are among the most lethal childhood tumors. While therapeutic approaches were largely adapted from adult treatment regime, significant biological differences between pediatric and adult gliomas exist, which influence the immune microenvironment and may contribute to the limited response to current pHGG treatment strategies. We provide a comprehensive transcriptomic analysis of the pHGG immune landscape using single-cell RNA sequencing and spatial transcriptomics. We analyze matched malignant, myeloid, and T cells from patients with pediatric diffuse high-grade glioma (HGG) or high-grade ependymoma, examining immune microenvironment distinctions after chemo-/radiotherapy, immune checkpoint inhibition treatment, and by age. Our analysis reveals differences in the proportions of pediatric myeloid subpopulations compared to adult counterparts. Additionally, we observe significant shifts toward immune-suppressive environments following cancer therapy. Our findings offer valuable insights into potential immunotherapy targets and serve as a robust resource for understanding immune microenvironmental variations across HGG age groups and treatment regimens.

Genetic screening of FFPE breast cancer biopsies for the BRCA1-185delAG mutation in Trinidad and Tobago

Objective

To investigate whether the quality and quantity of genomic DNA harnessed from existing formalin-fixed paraffin-embedded (FFPE) breast cancer biopsy tissue samples in the public health system of Trinidad and Tobago (T&T) were sufficient for downstream genetic testing and to investigate the occurrence of the common breast cancer susceptibility gene 1 (BRCA1) mutation, BRCA1-185delAG, in these samples.

Methods

Genomic DNA was extracted from 67 FFPE samples using a standard protocol (Qiagen). Samples were genotyped using polymerase chain reaction (PCR) and Sanger sequencing.

Results

The genomic DNA was highly fragmented in the 250-500 bp range. The quality and quantity only allowed testing of one variant. This study successfully genotyped 34 of 67 FFPE breast cancer tissue biopsy samples for the BRCA1-185delAG mutation. This mutation was not detected in the 34 samples.

Conclusion

Existing FFPE cancer tissue biopsies in the public health system in T&T are of limited utility for genetic testing. The absence of the BRCA1-185delAG mutation in the limited number of breast cancer samples tested does not preclude its existence in this population. Further investigations are needed to determine the extent of clinically relevant breast cancer-associated mutations in this population.