Comprehensive genomic profiling (CGP) tests have been covered by insurance in Japan since 2019, and their use in cancer genomic medicine (CGM) has expanded since then. Although extensive data are available from core hospitals, real-world data from community-based cooperative hospitals are limited. Using data from 514 consecutive patients with advanced cancer who underwent CGP testing at our institution between June 2019 and March 2025, we investigated the proportion of cases receiving therapeutic recommendations, the rate of drug administration based on CGP test results, and the prevalence and management of presumed germline pathogenic variants (PGPVs). The most common cancer sites were the pancreas (18.7%), breast (16.9%), bowel (14.6%), lung (12.8%), and prostate (12.5%). An expert panel made up of molecular oncologists recommended 360 targeted therapies for 311 patients (60.5% of the total cohort). Ultimately, 80 patients (15.6%) received matched therapy, among whom 56 received medication under health insurance coverage, 22 through clinical trials, and 2 via the patient-requested medical treatment system. PGPVs were identified in 68 patients (13.2%). After discussion by the expert panel, confirmatory germline testing was offered to patients with PGPVs, and subsequent germline testing confirmed pathogenic variants in 18 patients (3.5% of the total cohort). The proportion of patients who received targeted therapy at our cooperative hospital was comparable to proportions reported from core hospitals. However, disease progression was a significant barrier to accessing targeted therapies and genetic counseling. To maximize the benefits of CGM, the timing of CGP testing must be optimized and collaboration across departments and institutions must be strengthened.
Background. Our recent findings indicate that the rough form of the Mycobacterium abscessus complex (MABC) is associated with worse clinical outcomes compared to the smooth variant. The glycopeptidolipid (GPL) locus has been considered vital for this transition; however, this has only been shown during in vitro selection. Thus, we aimed to investigate genetic differences between the morphotypes among clinical isolates.Methods. Whole-genome sequencing (WGS) by Oxford Nanopore was applied to rough and smooth clinical MABC strains (n=10), including laboratory strains and in vitro exposure to nitric oxide (NO). Comparative genomic analysis, methylation and pangenome analysis were used to investigate the orthologs and unique protein clusters in relation to morphotype.Results. WGS analysis showed high average nucleotide sequence identity (>98%), but genetic variants compared to the reference genome ranged from 1,433 to 27,025, and these differences did not correlate with morphotype. Among clinical isolates, smooth MABC clustered and were separated from the rough isolates. In both rough and smooth phenotypes, random genetic variations that could not separate the morphotypes were detected mainly in the nrps of the GPL loci. The major protein-cluster differences between smooth (n=123) and rough (n=22) clinical isolates were observed in key genes outside the GPL locus, such as fabH, pks15, fadD29, otaA, mabA, lysX and acdA, primarily involved in fatty acid biosynthesis and transporter systems. Repeated NO exposure, serving as a proxy for host-related stress, induced a rough phenotype by altering the acyl desaturase DesA1 protein, which is involved in fatty acid synthesis.Conclusion. By analysing clinical MABC isolates, we show that morphotype variation cannot be explained by the GPL locus only. Unique genes involved in fatty acid biosynthesis were identified, informing further investigation into mechanisms distinguishing smooth and rough morphotypes of clinical MABC isolates.
Soft-tissue tumors are rare mesenchymal neoplasms characterized by extensive morphologic and genetic heterogeneity. Advances in molecular pathology have transformed their diagnosis, classification, and therapeutic management. Recurrent genomic alterations such as gene fusions, mutations, amplifications, and epigenetic changes define distinct tumor subtypes, guiding targeted therapy. Modern diagnostic platforms, from fluorescence in situ hybridization to next-generation and methylation-based sequencing, enable precise molecular characterization of these tumors. Integration of molecular and genomic data will continue to inform diagnosis, prognosis, and treatment response. Emerging technologies, including circulating biomarkers and artificial intelligence, further expand the role of molecular pathology in soft-tissue tumor care.
Thyroblastoma is a rare and highly aggressive embryonal thyroid malignancy typically associated with DICER1 alterations. However, DICER1-wildtype cases remain poorly characterized at the molecular level. We report a case of aggressive thyroblastoma in a 62-year-old male, negative for canonical DICER1 RNase IIIb mutations. Comprehensive genomic profiling was performed using Oxford Nanopore long-read sequencing, followed by integrative bioinformatic and pathway-level analyses. Molecular analysis revealed an alternative oncogenic signature characterized by an EIF1AX p.Lys3_Lys5dup duplication, TERT alterations (promoter C228T and coding p.C42R), and an AGK-BRAF fusion predicted to drive constitutive MAPK/ERK signaling. Functional enrichment analyses highlighted dysregulation of translational initiation, telomere maintenance, and mitogenic pathways, alongside potential immune-escape mechanisms linked to DUX4 activation. Clinically, the tumor exhibited a triphasic morphology, extensive locoregional infiltration, pulmonary metastases, and only transient response to chemotherapy. These findings expand the molecular spectrum of thyroblastoma beyond the canonical DICER1-driven paradigm and suggest that DICER1-wildtype cases may represent a distinct biological subgroup. The identification of alterations affecting TERT and MAPK pathways highlights potential therapeutic vulnerabilities and supports the clinical value of comprehensive genomic profiling in ultra-rare thyroid malignancies.
Spermatogenesis is a highly coordinated male developmental process essential for passing on genetic information and fertility. The process features a series of complex cellular and genomic transitions. The main objective of this review is to provide a synthesis of changes single-cell genomics have brought to the male germline. This review begins with an account of the journey from rudimentary, low resolution, and throughput microarray technologies to the advanced and sophisticated, high throughput single-cell RNA sequencing (scRNA-seq) technologies that have provided the means for the generation of extensive and comprehensive "cell atlases" of the testis. The review focuses on the resolution of long-standing controversies associated with the spermatogonial stem cells (SSCs) niche regarding continuum of germ cell differentiation, and germ cell differentiation and stem cell specification. The frontiers of single-cell based DNA techniques such as Single-Cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) and single-cell DNA methylation will then be discussed. We focus on the perinatal period crucial for the epigenetic priming of the foundational stem cell pool and chromatin remodeling that facilitates the histone-to-protamine transition. The regenerative capacity of the germline and the single-cell identified subsets and metabolic gates that are capable of restoring the ability to conceive post-injury tissues are also explored. Finally, we will go over the prospective views on the use of multi-omics and new spatial transcriptomics. These tools not only provide molecular components of interest within the cells, but also the cellular constituents of the seminiferous tubule and their spatial location within the tubule. This novel information will help translate the molecular discovery into potential clinical applications for male infertility treatment.
G protein-coupled receptors (GPCRs) constitute the largest membrane receptor family in the human genome and serve as key regulators of cell signaling, homeostasis, and pharmacologic response. Beyond their classical role in mediating extracellular stimuli through G-protein-dependent and independent pathways, which have a pivotal role of GPCR-mediated signaling pathways, including the cAMP-PKA/EPAC, IP3/PLC, PI3K/Akt/mTOR, and ERK/MAPK cascades, in driving oncogenic proliferation, apoptosis resistance, and metastasis. Furthermore, GPCRs are implicated in tumorigenesis through diverse molecular mechanisms, in which GPCR dysregulation contributes to cancer initiation and progression via aberrations at multiple genomic and regulatory levels, including copy number variations (CNVs), epigenetic modifications, post-transcriptional, and post-translational modifications. Despite their extensive biological roles and druggability, targeting GPCRs in cancer therapy has yielded promising outcomes, notably via SMO and chemokine receptor inhibitors. Overall, we aim to bridge the gap between fundamental GPCR signaling biology and clinical oncology. We integrated the deregulated expression and pathways of GPCR oncogenic processes, with the potential to be actionable biomarkers for tumor screening and clinical practices using GPCR drugable targets. Therefore, we represent and highlight pathway-specific signaling pathways with their tumor microenvironment interactions, drug combination strategies, and molecular imaging and theranostics applied in clinical practice and precision medicine.
Stripe rust caused by Puccinia striiformis f. sp. tritici (Pst), represents one of the most significant challenges to the world's wheat production. This study aimed to investigate five aggressive physiological races of Pst impacting significant wheat cultivars in Egypt's northern Delta, which are essential for breeding programs. Moreover, the study evaluated the antifungal activity and mechanisms of action of chitosan nanoparticles, Trichoderma harzianum, and Sargassum latifolium against Pst using molecular docking analysis. During the 2024 growing season, an increase in the virulence of newly identified aggressive Pst races in Egypt was detected. A total of 20 and 23 races were recognized from 89 out of 132 samples in 2023 and 86 out of 115 samples in 2024, respectively. In addition, twenty Egyptian wheat cultivars and fifty-two CIMMYT nursery lines were screened at the Sakha Agricultural Research Station for resistance to five aggressive stripe rust races at both seedling and adult stages. The results revealed that most cultivars were susceptible, with only two (10%) and five (25%) displaying resistance. Among the CIMMYT entries, 17 (33%) and 21 (40%) confirmed resistance in 2023 and 2024, respectively. Single nucleotide polymorphism (SNP) markers were used to identify the five Pst races, and phylogenetic analysis was conducted using representative fungal species from genomic databases. The five aggressive races were deposited in the GenBank database under accession numbers PV983376, PV983377, PV983378, PV983379, and PV983380. Biological treatments using S. latifolium, T. harzianum, and chitosan nanoparticles significantly decreased stripe rust disease severity. These findings recommend that such treatments can support high-quality wheat flour production and serve as safe, environmentally friendly alternatives to synthetic fungicides. Molecular docking analysis further elucidated the mechanisms of antifungal action, particularly highlighting the effectiveness of S. latifolium and T. harzianum against Pst races. Overall, this investigation exhibits strong potential for improving wheat cultivars with enhanced yield and resistance to aggressive stripe rust races, contributing to sustainable disease management strategies.
Carbapenem-resistant Acinetobacter baumannii (CRAB) has emerged as a major global clinical threat, particularly in low- and middle-income countries where treatment options remain limited. This study investigated the genomic characteristics and clonal relatedness of CRAB clinical isolates recovered during the implementation of the National Action Plan on Antimicrobial Resistance (NAP-AMR) in Mwanza, Tanzania. Whole-Genome Sequencing was performed on six phenotypically carbapenem-resistant A. baumannii isolates obtained from blood (n = 3), urine (n = 2) and pus (n = 1) samples collected at Bugando Medical Centre, a tertiary referral hospital in northwestern Tanzania. Genomic analyses included sequence typing, antimicrobial resistance gene identification and virulence profiling using web-based bioinformatics tools. Phylogenetic relationships were inferred using core-genome MLST (cgMLST). Three STs were identified, with a predominance of ST-1325 (Oxford scheme)/ST-374 (Pasteur scheme), (66.7%; n = 4). Other STs included ST-2822OX/ST-374PAS (n = 1) and ST-2323OX/ST-1PAS (n = 1). The internationally recognized high-risk lineage, ST-1PAS, carried bla OXA-69 and mercury-resistance genes (merA/D/E/T). All isolates exhibited multidrug-resistant phenotypes fully consistent with their genotypic profiles. Carbapenem resistance was driven by bla OXA-259 (66.7%; n = 4) in ST-1325OX/ST-374PAS isolates. Virulence determinants associated with adhesion, biofilm formation, immune evasion and iron acquisition were detected in all isolates. Mobile genetic elements, including transposons (83.3%), integrons (83.3%) and insertion sequences (100%), were common, predominantly Tn6292, In2-10 and ISAba26, respectively. Phylogenetic analysis revealed clonal relatedness among the four ST-1325 isolates recovered from urine and blood samples. CRAB isolates in our setting were dominated by ST-1325OX/ST-374PAS carrying bla OXA-259, with evidence of clonal relatedness suggesting possible transmission, underscoring the importance of strengthening infection prevention and genomic surveillance.
The understanding of the biologic basis of mature lymphoid neoplasms has been impacted through the sequential integration of emerging molecular technologies. Early techniques such as Southern blotting were foundational in establishing molecular hematopathology by demonstrating antigen receptor gene rearrangements and supporting the identification of lymphoid clonality. The development of FISH and PCR allowed for sensitive detection of specific translocations. Most notably, mutation detection via high-throughput sequencing and its various additional applications to DNA and RNA has transformed hematopathology, enabling comprehensive genomic profiling into not only routine diagnostics but also determining prognosis and guiding therapy for these diverse neoplasms.
Colorectal carcinoma (CRC) is the most prevalent malignancy of the gastrointestinal tract and remains a leading cause of cancer-related illness and death worldwide. Recently, new treatment strategies have emerged with the identification of important biomarkers in CRC. As the emphasis on precision medicine in oncology intensifies, testing tumor specimens for key genomic alterations is becoming standard-of-care. This article seeks review the key molecular changes in CRC with important therapeutic implications.
NASA cleanrooms, which are critical for assembling space mission components, are maintained under stringent decontamination protocols to minimize biological contamination. These environments are characterized by nutrient-poor and oligotrophic conditions, leading to low microbial loads. Despite extensive cleaning, oligotrophs capable of surviving in such conditions continue to persist, often remaining undetected due to their low abundance, resistance to environmental stresses, and difficulties in biomolecule extraction. Even with shotgun metagenome sequencing technologies, these microbes may go undetected or be underrepresented due to their robust cell walls and the absence of reference genomes in publicly available databases. Over a 6-month study of Mars 2020 mission cleanrooms, 182 bacterial strains belonging to 19 families were identified using a whole-genome sequencing (WGS) approach. Among these, 14 novel Gram-positive species were discovered, including eight spore formers. Though the novel species comprised only 0.001% of the sequencing data, their successful cultivation allowed for functional characterization. Through WGS data mining, genomic traits associated with resilience in extreme conditions were revealed. These species were found to be involved in nitrogen cycling, carbohydrate metabolism, and radiation resistance, traits essential for survival in extreme environments. Furthermore, 12 biosynthetic gene clusters were identified, including those linked to ectoine and [Formula: see text]-poly-L-lysine production, suggesting potential biotechnological applications. These findings highlight the hidden microbial diversity within cleanrooms and emphasize the necessity of advanced detection strategies. A better understanding of these microbes will provide insights into extremophiles with applications in biotechnology, medical research, and life support systems for future space exploration missions.IMPORTANCEDespite strict decontamination protocols, NASA cleanrooms harbor low-biomass microbial communities adapted to nutrient-poor environments. These oligotrophic microbes often go undetected in shotgun metagenomics methods due to their low abundance, resistance to lysis, and lack of reference genomes. Standard shotgun metagenome sequencing methods fail to retrieve them, as dominant microbial DNA overshadows rare species. Over 6 months of monitoring Mars 2020 mission cleanrooms, 182 bacterial strains from 19 families were identified, including 14 novel Gram-positive species, 8 of which were spore formers. Though present at 0.001% abundance in sequencing data, we successfully cultured them, enabling functional characterization. These microbes exhibited roles in nitrogen cycling, carbohydrate metabolism, and radiation resistance, with 12 biosynthetic gene clusters linked to ectoine and [Formula: see text]-poly-L-lysine production. These findings highlight the previously underestimated microbial diversity in cleanrooms and emphasize the need for advanced detection strategies to explore extremophiles with applications in biotechnology and space exploration.
This article summarizes the molecular landscape of epithelial and non-epithelial ovarian tumors, integrating current genomic and immunophenotypic data. High-grade serous carcinomas are defined by TP53 and homologous recombination defects, while low-grade serous, mucinous, endometrioid, and clear cell carcinomas exhibit pathway-specific mutations such as MAPK/MEK and PI3K/AKT pathway alterations. Sex cord-stromal tumors are characterized by FOXL2, DICER1, and CTNNB1 alterations. The article also outlines hereditary cancer syndromes affecting ovarian tumorigenesis, emphasizing tumor predisposition associated with BRCA1/2, Lynch syndrome, Peutz-Jeghers syndrome, and DICER1.
The identification of actionable genomic alterations in lung cancer represents the established standard of care, serving as the foundation for selecting the most efficacious therapies. As the scope of molecular and biomarker testing in lung cancer continues to evolve, pathologists play a critical role in determining which specimens are appropriate for testing, identifying the relevant molecular targets, and selecting the optimal methodologies. This article will summarize the biomarker landscape in non-small cell lung cancer (NSCLC), current recommendations for their implementation, and how to maximize the diagnostic and predictive value of the limited tissue samples obtained from patients with NSCLC.
Recent advances in molecular profiling, including next-generation sequencing and bioinformatic approaches, have enabled detailed characterization of tumor biology and facilitated patient stratification based on prognostic and predictive factors associated with clinical outcomes and therapeutic response. This article summarizes key biomarkers with established clinical relevance in kidney, bladder, and prostate cancers. In bladder and prostate cancer, novel insights into tumor biology have reshaped therapeutic strategies and supported the approval of targeted therapies, thereby enhancing patient care. Selecting appropriate molecular tests-such as FGFR screening in urothelial carcinoma and BRCA1/2 testing in prostate cancer-has become critical for guiding treatment decisions.
Prostate Cancer-3 (PC-3) cells, commonly used as a model for aggressive, androgen-independent prostate cancer, display numerous genetic alterations that contribute to advanced disease, including the loss of tumor suppressors and dysregulated inflammatory signaling. Recent evidence has highlighted the pleiotropic roles of lipocalin 2 (LCN2) in promoting tumor cell proliferation, adhesion, and stress resistance. This study aimed to investigate the functional and molecular effects of LCN2 depletion in PC-3 cells. We conducted a genetic analysis of both the parental PC-3 cell line and a newly created LCN2-deficient PC-3 clone #1 (PC-3 LCN2-KO#1), developed using CRISPR/Cas9 technology. Short tandem repeat (STR) analyses confirmed the authenticity and lineage of each cell line, while next-generation sequencing coupled with RT-qPCR validation was used to identify differentially expressed genes and any potential genomic changes resulting from the CRISPR/Cas9 editing process. Our analysis aligned with our previous findings showing that LCN2 is involved in inflammation, endoplasmic reticulum stress responses, and cytoskeletal organization. Previously we have shown that LCN2-deficient cells exhibited decreased invasiveness, disrupted F-actin dynamics, and increased sensitivity to stress-inducing conditions. Consistent with these observations, spectral karyotyping (SKY) and analysis of spontaneously occurring micronuclei revealed an elevated level of chromosomal aberrations in the LCN2-deficient cell line. These results emphasize the significance of LCN2 in driving prostate cancer aggressiveness and provide a foundation for exploring targeted interventions that disrupt LCN2-mediated pathways in advanced disease.
Understanding the genetic regulation of circulating protein levels can provide new insights into disease mechanisms. Here, we present the largest proteogenomic study to date (n = 78,664 participants across 38 studies), identifying >24,000 protein quantitative trait loci (QTLs) associated with 1,116 proteins, acting near to (n = 5,040) or distant (n = 19,698) from the cognate gene. Using machine learning-guided effector gene assignment, we provide genetic evidence for pathways, cell types, and tissues that modulate circulating protein levels, highlighting N-linked glycosylation as an important regulatory pathway. We demonstrate that genetic instruments of protein production/function ("cis") versus modulation ("trans") reveal distinct phenotypic insights. We identify proteins as candidates for drug targets and engagement (e.g., plasma furin and cardiovascular diseases) by comparing cis-based genetic evidence with protein-disease associations. Systematic triangulation of trans-protein QTLs (pQTLs) with genetic and protein associations across many diseases highlights potential drug repurposing opportunities, e.g., tyrosine kinase 2 (TYK2) inhibitors for rheumatoid arthritis. Our multi-cohort meta-analyses generate proteogenomic insights into disease mechanisms and new treatment opportunities.
Cyanobacteria are promising candidates for sustainable bioproduction due to their ability to fix CO2 via photosynthesis to produce valuable compounds. However, efforts toward their genetic engineering remain limited by inefficient, strain-specific transformation methods. In this study, we systematically evaluated BPP Bioportides™, a protein-based DNA delivery system, as a novel transformation approach across multiple cyanobacterial strains, including Synechocystis sp. PCC 6803, Synechococcus elongatus PCC 7942, and Synechococcus sp. UTEX 3153. BPP Bioportide™ variants BP-17 and BP-12 significantly improved transformation efficiency of both plasmid and linear DNA, even with minimal DNA input of 10 ng, surpassing conventional methods and enabling modification of previously non-model strains. Optimization revealed a narrow window for DNA uptake and identified key factors influencing genomic integration, such as DNA type, host ploidy, and selection conditions. Successful double homologous recombination and partial to full genomic segregation were validated by colony PCR. BPP Bioportide™-mediated transformation offers a versatile and efficient platform for cyanobacterial genome engineering, supporting advances in synthetic biology and carbon-neutral biotechnology.
Hemophilia A is an X-linked recessive bleeding disorder caused by a deficiency or dysfunction of factor VIII (FVIII), affecting approximately 1 in 5,000 males globally, including those in northern India. Accurate carrier detection is vital for genetic counseling and early diagnosis. This study aimed to assess the allele frequencies of three key intronic polymorphisms-IVS7-SNP (G/A), rs4898352 (T/A) in intron 18 (Bcl-I), and rs4074307 (C/T) in intron 19 (Hind-III)-in Indian children with Hemophilia A and evaluate their utility in carrier detection and linkage analysis. A total of 205 unrelated male children with Hemophilia A, representing 195 families from Eastern and Northern-Central India were included. Diagnosis was confirmed via FVIII assay. Genomic DNA was extracted from peripheral leukocytes. Genotyping of the three selected intronic polymorphisms in the F8 gene was carried out using ARMS-PCR. The positive allele frequencies observed for IVS7-SNP, Bcl-I, and Hind-III were 0.10, 0.53, and 0.36, respectively. The negative allele of IVS7-SNP was found to be more prevalent among affected siblings. Family histories frequently revealed multiple affected individuals and hemophilia-related deaths, emphasizing the hereditary burden of the disorder in these regions. The distribution of the studied polymorphisms is consistent with global heterozygosity patterns and underscores their potential role in carrier screening and linkage analysis. These findings provide a feasible genetic tool for early diagnosis and counseling in Hemophilia A, particularly in low-resource settings where direct mutation analysis is limited.
Pancreatic cancer represents one of the most lethal tumors, characterized by an immunosuppressive microenvironment and a lack of cytotoxic immune cell infiltrates, which confer resistance to immunotherapy. Here, we demonstrate that deletion of poly(ADP-ribose) polymerase 2 (PARP2) in a Myc-driven mouse model of pancreatic cancer delays tumor progression and increases survival. Mechanistically, PARP2 loss induces enrichment of pathways associated with genomic instability and replicative stress, leading to increased γH2AX, chromosomal instability, and micronuclei accumulation. In addition to these tumor-intrinsic effects, PARP2 deletion reshapes the tumor microenvironment, promoting infiltration of cytotoxic T and natural killer cells while reducing immunosuppressive cell populations, enhancing antitumor cytotoxicity. These findings are recapitulated in a KrasG12D-driven orthotopic pancreatic ductal adenocarcinoma model. Collectively, our data support selective PARP2 inhibition as a promising therapeutic strategy for pancreatic cancer by impairing genome integrity and boosting antitumor immune response, thereby opening potential avenues for combating this devastating disease.
Glioblastoma (GBM) heterogeneity limits the efficacy of EGFR-targeted therapies. Here, we present a spatially stratified single-cell atlas of IDH-wildtype GBM to dissect the impact of EGFR amplification on tumor architecture. We demonstrate that EGFR amplification disrupts the spatial coupling between evolutionary state and anatomical location, resulting in premature acquisition of invasive phenotypes-a phenomenon we term "accelerated evolutionary velocity." Unlike nonamplified tumors which maintain a strict "Core-to-Margin" developmental gradient, malignant cells in EGFR-amplified tumors acquire invasive mesenchymal traits preemptively regardless of their spatial niche. This accelerated evolution parallels the Core behaving as a "genotoxic stress reservoir" characterized by elevated chromosomal instability (CIN) (p < 2.2 × 10-16). This genotoxic stress coincides with the emergence of a localized tumor-myeloid axis and an immune-suppressive niche. Using the PriorityScore2 framework, we prioritized Periostin (POSTN) as a top-tier clinically relevant candidate. In the high-CIN environment of EGFR-amplified GBM, in silico network perturbation suggested that POSTN may function as a candidate modulator of mitotic fidelity, potentially buffering against lethal genomic instability while sustaining rapid clonal evolution. Validated across multicenter cohorts, POSTN showed robust upregulation, strong diagnostic performance (AUC = 0.961), and significant prognostic relevance, emerging as a potential therapeutic vulnerability linking accelerated evolution with immune privilege in the GBM ecosystem.