Human Mutation最新文献

While hypoxia-driven nucleolar stress (NS) has been recognized as a critical modulator of the immunosuppressive tumor microenvironment in clear cell renal cell carcinoma (ccRCC), its mechanistic contribution to disease progression remains poorly defined. To address this gap, we systematically mapped NS-associated molecular landscapes through integrated spatial transcriptomics and single-cell RNA sequencing of ccRCC specimens. Our analysis stratified tumors into two distinct NS subtypes, revealing that high-NS tumors exhibit aggressive clinical behavior, elevated expression of immunosuppressive checkpoints, and significantly reduced survival. At single-cell resolution, high-NS malignant cells displayed enhanced proliferative activity, glycolytic metabolic reprograming, and marked chromosomal instability. Mechanistic investigations demonstrated that hypoxia-induced ETS1 activation orchestrates NS via the MYC/NPM1/DDX17 signaling axis, directly promoting tumor proliferation and metabolic adaptation in preclinical models. Spatial multiomics further uncovered coordinated niche formation between high-NS cells and OLR1⁺ macrophages, with ligand–receptor profiling identifying the EDN1–EDNRA–OLR1 axis as a central mediator of this immunosuppressive crosstalk. Functional validation in syngeneic mouse models confirmed that ETS1 overexpression accelerates tumor growth while enriching OLR1⁺ macrophages with immunosuppressive phenotypes. Clinically, high OLR1⁺ macrophage infiltration correlated with shorter survival across independent cohorts. These findings establish a hypoxia–ETS1–NS–macrophage axis as a key mechanism sustaining ccRCC progression and highlight actionable targets for disrupting protumorigenic immune niches through modulation of the NS pathway.

Background: Vimentin (VIM), a cytoskeletal protein implicated in tumor progression, has been associated with poor prognosis in B cell lymphomas. Alternative polyadenylation (APA), a posttranscriptional mechanism that modulates mRNA isoforms via 3 ^′UTR length changes, is frequently dysregulated in cancer. The interaction between VIM and APA in B cell lymphoma remains poorly understood.

Methods: We performed RNA-seq, APA analysis (DaPars), and proteomic profiling in wild-type and VIM-knockout (VIM-KO) B cell lymphoma cells (A20 and M12). Functional assays including CCK-8, EdU, Western blot, and ARVCF overexpression were used to explore the regulatory axis involving APA and mTOR signaling.

Results: VIM deletion in B cell lymphoma cells triggered widespread transcriptome remodeling, inducing 4089 APA shortening events that preferentially targeted prosurvival pathways, for example, mTORC1, G2-M checkpoint. Strikingly, RRAGA—a critical mTOR activator—underwent 3 ^′UTR shortening, concomitant with ARVCF downregulation in proteomic profiles. Functional rescue experiments demonstrated ARVCF’s dual role in maintaining RRAGA 3 ^′UTR length and suppressing mTOR-EIF4G1 signaling, ultimately inhibiting lymphoma proliferation.

Conclusion: This study reveals a novel VIM–ARVCF–RRAGA–mTOR axis in B cell lymphoma, linking cytoskeletal disruption to APA-mediated oncogenic signaling. VIM loss drives APA shortening and mTOR activation via ARVCF downregulation, promoting lymphoma progression. These findings offer mechanistic insight and potential targets for therapeutic intervention.

Colon adenocarcinoma (COAD) is a particularly aggressive cancer type, frequently identified at a later stage. Thus, it is crucial to enhance our understanding of the fundamental mechanisms that govern COAD cellular behavior and to perform extensive research into the biological foundations underlying its development, progression, invasion, and metastasis. We initially discovered NOL3 as a significant gene influencing COAD metastasis through the application of the weighted gene coexpression network analysis algorithm using the TCGA-COAD dataset. This was succeeded by an assessment of NOL3’s expression levels and prognostic significance. Moreover, we investigated the biological roles of NOL3 utilizing transcriptomic data. Our results demonstrate significant associations between NOL3 and immune infiltration in COAD, as well as sensitivity to chemotherapy. Furthermore, we utilized the tumor immune dysfunction and exclusion (TIDE) algorithm to evaluate how various cohorts responded to immune checkpoint therapies. Ultimately, the influence of NOL3 on the metastasis of COAD cells was confirmed through in vitro experiments. Our results indicate that NOL3 can promote COAD metastasis, and its underlying mechanism may be associated with DNA methylation. In summary, NOL3 has been identified by us as a key biomarker for COAD metastasis.

Colorectal cancer (CRC) ranks among the most common malignant tumors worldwide, with the metabolism of fatty acids being crucial for its development and progression. Altered fatty acid metabolism is a well-established metabolic characteristic of malignant tumors, including CRC. A complex and reciprocal relationship exists between fatty acid metabolism and CRC. On one side, the emergence and advancement of CRC can trigger a reprogramming of fatty acid metabolism. To fulfill the requirements of rapid cell division and survival, cancer cells increase both the synthesis and uptake of fatty acids while also suppressing their oxidation. Conversely, modifications in fatty acid metabolism can affect CRC, as abnormal fatty acid byproducts may activate signaling pathways that foster tumor cell proliferation, thus enhancing tumor progression. Understanding the interplay between fatty acid metabolism and the early stages and advancement of CRC, in conjunction with its relationship with the tumor microenvironment, is a vital area for future investigation. This article reviews the most recent discoveries concerning the impact of fatty acid metabolism on CRC progression, with the objective of supplying a solid theoretical framework and innovative perspectives for additional research and treatment of this condition.

Abdominal aortic aneurysm (AAA) is a serious vascular condition that significantly endangers the lives of patients. Although there have been improvements in early detection and treatment methods, considerable challenges persist regarding the timely identification and evaluation of risk associated with this disease. Therefore, there is an immediate requirement for novel biomarkers that can enhance the early diagnosis and risk evaluation of AAA, thus allowing for more accurate and individualized medical interventions. In this study, we identified key diagnostic markers for AAA using various machine learning algorithms, and we explored the functions of these genes in AAA through gene enrichment analysis. A diagnostic model for AAA was constructed based on multiple machine learning algorithms, with the random forest algorithm highlighting the central role of ARHGAP9. In vitro experiments confirmed the influence of ARHGAP9 on vascular smooth muscle cells (VSMCs). Our findings indicate that the key genes identified are associated with the immune microenvironment and metabolism in AAA samples. The validated diagnostic model exhibited excellent predictive performance. Knockdown of ARHGAP9 significantly inhibited the proliferative capacity of VSMCs. In conclusion, our results suggest that ARHGAP9 may serve as a diagnostic and therapeutic marker for AAA.

Background: Bladder urothelial carcinoma (BLCA) is a prevalent malignant tumor known for its high recurrence rates and limited therapeutic efficacy. Cellular senescence has been extensively shown to inhibit tumorigenesis via cell cycle arrest. Consequently, the identification of senescence-associated biomarkers is essential for enhancing the diagnosis, prognosis, and immunotherapeutic outcomes of BLCA.

Method: This study integrated the TCGA-BLCA and GSE13507 datasets to analyze senescence-related genes. ConsensusClusterPlus was employed for cluster analysis, while immune infiltration was assessed using CIBERSORT. A diagnostic and prognostic model for BLCA was developed and validated through the combination of various machine learning algorithms. Experimental validation was conducted using qRT-PCR, colony formation, and Transwell assays to evaluate the functional role of PAQR4.

Result: Our study revealed that aging-related samples demonstrated improved survival rates and a lower incidence of high-grade tumors. Cluster analysis identified two distinct subgroups of BLCA characterized by unique immune infiltration profiles and varying responses to immune checkpoint blockade. The diagnostic and prognostic models developed from aging-related genes were subsequently validated. Notably, PAQR4 was identified as a critical aging-related gene linked to poor prognosis and an immunosuppressive microenvironment. The knockdown of PAQR4 significantly inhibited the proliferation and metastasis of BLCA cells.

Conclusion: PAQR4 is a novel biomarker and therapeutic target for BLCA, influencing cellular senescence, immune evasion, and metastasis. This study provides insights into the senescence-related mechanisms and offers tools for precision diagnosis and the optimization of immunotherapy in BLCA.

S. S. Cornelis, M. Bauwens, L. Haer-Wigman, et al., “Compendium of Clinical Variant Classification for 2,246 Unique ABCA4 Variants to Clarify Variant Pathogenicity in Stargardt Disease Using a Modified ACMG/AMP Framework,” Human Mutation 2023 (2023): 6815504, https://doi.org/10.1155/2023/6815504.

In the article titled “Compendium of Clinical Variant Classification for 2,246 Unique ABCA4 Variants to Clarify Variant Pathogenicity in Stargardt Disease Using a Modified ACMG/AMP Framework,” there was an error in Figure 1 artwork and caption. The corrected Figure 1 artwork and caption are shown below:

We apologize for this error.

Variants of uncertain significance (VUS) in the DNA mismatch repair (MMR) genes can confound the diagnosis and treatment of suspected Lynch syndrome (LS) patients. To aid the reclassification of VUS, we developed the in cellulo analysis of MMR variants (inCAMA) and used known control variants to calibrate this assay such that results can be readily applied as functional evidence by expert classification panels. We used CRISPR gene engineering to introduce known pathogenic and benign variants into the MSH6 or MSH2 loci in human embryonic stem cells and assessed their effects on cellular MMR repair and damage response functions. Our functional assay successfully discerned known pathogenic and benign variants. Using these results and performing a linear regression analysis with available odds of pathogenicity scores for the known calibration variants, we created equations that can generate a functional odds of pathogenicity score for any future MSH6 or MSH2 variant tested. In summary, inCAMA represents a new, calibrated assay for testing the function of virtually any MSH6 or MSH2 variant. The conversion of assay results directly into odds of pathogenicity scores makes it possible to use any PS3 or BS3 evidence strength level toward the reclassification of VUS.

Over the past decade, genome-wide association studies (GWASs) have found genetic variants associated with elevated risk for nonsyndromic orofacial cleft (NSOFC). In the post-GWAS era of NSOFC genetic research, an important aim is to identify the pathogenic variants that influence craniofacial development processes, towards understanding how they lead to disease manifestation. However, two major challenges hinder the translation of GWAS results into a mechanistic understanding. Firstly, it is uncertain whether the variants pinpointed by GWAS represent the underlying pathogenic variants; secondly, the bulk of genetic variants identified through GWAS are situated in noncoding regions of the genome, complicating their biological interpretation. Presently, research on noncoding genetic variants associated with NSOFC predominantly centers on variants located in transcriptional regulatory elements. These variants modulate transcription, subsequently altering the expression of downstream target genes and disrupting gene regulatory networks. We provide a systematic summary of the recent NSOFC-associated GWAS findings for the first time. With a particular focus on variants located in noncoding regions, we delve into current statistical methods and functional approaches for identifying and validating causal variants, aiming to bridge the gap between genetic variants identified by GWAS and their underlying pathogenic mechanism responsible for NSOFC. Deciphering causal variants underlying NSOFC offers valuable clinical insights that may advance early diagnosis, enhance risk stratification, and facilitate the discovery of novel therapeutic targets.

Dyskeratosis congenita (DC) is an inherited bone marrow failure syndrome characterized by defects in telomere biology and clinical manifestations such as nail dystrophy, skin pigmentation abnormalities, and mucosal leukoplakia. Here, using whole exome sequencing (WES), whole genome sequencing (WGS), optical mapping sequencing (OGM), third-generation sequencing, and mRNA sequencing, we diagnosed a participant with PARN gene complex compound heterozygous variants. In addition, protein structure simulation, immunohistochemistry, and western blot were conducted to investigate the structure and expression level of the PARN protein. WES revealed a maternal PARN variant, c.204G>T (p.Gln68His) (NM_002582.3). An insertion variant in the PARN gene from the father was identified by OGM and mRNA sequencing. Third-generation sequencing results determined the insertion position of the SINE-VNTR-Alu (SVA) transposon and its size (2537 bp), which was found to lead to a premature stop codon (p.Gly469delinsGlu∗). The PARN protein level of the parents was reduced due to complex heterozygous variants. Overall, OGM diagnosed the structural variants of the participant with DC, supplementing the disease variant spectrum of DC. This case highlights a novel disease-causing structural variant and the importance of transposon analysis in a clinical diagnostic setting.