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Q RadFusion: Hybrid Quantum Classical Radiogenomic Framework for Breast Cancer Diagnosis.

BACKGROUND AND PURPOSE: Breast cancer remains the most common cancer in women worldwide, with early and accurate diagnosis critical for patient survival. Radiogenomics integrates imaging phenotypes with genomic profiles, offering a pathway to precision diagnostics. However, existing classical machine learning models often struggle with the high dimensionality and heterogeneity of multimodal data, leading to issues in calibration and reproducibility. This study presents Q RadFusion, a hybrid quantum-classical framework designed to enhance breast cancer diagnosis by fusing mammography and genomics data. METHODS: Q RadFusion was implemented on two publicly available datasets: CBIS-DDSM (2,600 curated mammography cases, TCIA) and TCGA-BRCA (1,000 genomic profiles, GDC). Imaging preprocessing included bias-field correction, segmentation, and harmonization, while genomic data underwent normalization and imputation. Feature selection was performed using the Quantum Approximate Optimization Algorithm (QAOA), and features were mapped into a quantum Hilbert space using Variational Quantum Circuits (VQC). For multimodal fusion, ResNet encoded mammography features, and a Transformer encoded genomic features. Patient-level and site-held-out splits were used for evaluation. RESULTS: Q RadFusion achieved an AUC of 0.96 and accuracy of 94%, outperforming baselines including CNN-LSTM, ResNet + XGBoost, and multimodal Transformers. Ablation studies confirmed the contribution of quantum components, with optimal performance observed at circuit depth, qubits, and QAOA layers. The model also demonstrated improved calibration and ~ 80% fewer parameters compared to deep fusion networks. CONCLUSION: Q RadFusion demonstrates that hybrid quantum-classical radiogenomic integration can deliver accurate, reproducible, and clinically meaningful diagnostic support for breast cancer, with strong potential for future clinical translation.

Breast Cancer↗

Prediction of clinical drug efficacy by classification of drug-induced genomic expression profiles in vitro.

Assays of drug action typically evaluate biochemical activity. However, accurately matching therapeutic efficacy with biochemical activity is a challenge. High-content cellular assays seek to bridge this gap by capturing broad information about the cellular physiology of drug action. Here, we present a method of predicting the general therapeutic classes into which various psychoactive drugs fall, based on high-content statistical categorization of gene expression profiles induced by these drugs. When we used the classification tree and random forest supervised classification algorithms to analyze microarray data, we derived general "efficacy profiles" of biomarker gene expression that correlate with anti-depressant, antipsychotic and opioid drug action on primary human neurons in vitro. These profiles were used as predictive models to classify naïve in vitro drug treatments with 83.3% (random forest) and 88.9% (classification tree) accuracy. Thus, the detailed information contained in genomic expression data is sufficient to match the physiological effect of a novel drug at the cellular level with its clinical relevance. This capacity to identify therapeutic efficacy on the basis of gene expression signatures in vitro has potential utility in drug discovery and drug target validation.

Algorithms↗

Revisiting the evolution of Mycobacterium bovis.

Though careful consideration has been placed towards genetic characterization of tubercle bacillus isolates causing disease in humans, those causing disease predominantly among wild and domesticated mammals have received less attention. In contrast to Mycobacterium tuberculosis, whose host range is largely specific to humans, M. bovis and "M bovis-like" organisms infect a broad range of animal species beyond their most prominent host in cattle. To determine whether strains of variable genomic content are associated with distinct distributions of disease, the DNA contents of M. bovis or M. bovis-like isolates from a variety of hosts were investigated via Affymetrix GeneChip. Consistent with previous genomic analysis of the M. tuberculosis complex (MTC), large sequence polymorphisms of putative diagnostic and biological consequence were able to unambiguously distinguish interrogated isolates. The distribution of deleted regions indicates organisms genomically removed from M. bovis and also points to structured genomic variability within M. bovis. Certain genomic profiles spanned a variety of hosts but were clustered by geography, while others associated primarily with host type. In contrast to the prevailing assumption that M. bovis has broad host capacity, genomic profiles suggest that distinct MTC lineages differentially infect a variety of mammals. From this, a phylogenetic stratification of genotypes offers a predictive framework upon which to base future genetic and phenotypic studies of the MTC.

Evolution, Molecular↗

Multiple genomic alterations including N-myc amplification in a primary large cell medulloblastoma.

The large cell (LC) subtype is a recently described histologic variant of medulloblastoma (Mb) associated with a rapid and aggressive clinical course. We describe the genomic profile of a LC-Mb tumor obtained from a patient who developed recurrent and fulminant disease despite 'good-risk' features at diagnosis and state- of-the-art multidisciplinary therapy. The tumor sample was analyzed using comparative genomic hybridization (CGH) and complementary molecular approaches. CGH revealed amplicons at chromosome bands 2p24-25, 2q12-22, and 17p11; losses of chromosomes 11q and 18; and low-level gains of 3q, 11p, 13q and 14q. Southern blot analysis confirmed N-myc amplification. No evidence of p53 mutation was detected. The genomic profile of this LC-Mb tumor sample revealed a distinctive pattern of genetic alterations including amplification of N-myc and anonymous oncogenes at chromosome bands 2q12-22 and 17p11. These genomic abnormalities are uncommon in other subtypes of Mb.

Blotting, Southern↗

Cell envelope stress response in Bacillus licheniformis: integrating comparative genomics, transcriptional profiling, and regulon mining to decipher a complex regulatory network.

The envelope is an essential structure of the bacterial cell, and maintaining its integrity is a prerequisite for survival. To ensure proper function, transmembrane signal-transducing systems, such as two-component systems (TCS) and extracytoplasmic function (ECF) sigma factors, closely monitor its condition and respond to harmful perturbations. Both systems consist of a transmembrane sensor protein (histidine kinase or anti-sigma factor, respectively) and a corresponding cytoplasmic transcriptional regulator (response regulator or sigma factor, respectively) that mediates the cellular response through differential gene expression. The regulatory network of the cell envelope stress response is well studied in the gram-positive model organism Bacillus subtilis. It consists of at least two ECF sigma factors and four two-component systems. In this study, we describe the corresponding network in a close relative, Bacillus licheniformis. Based on sequence homology, domain architecture, and genomic context, we identified five TCS and eight ECF sigma factors as potential candidate regulatory systems mediating cell envelope stress response in this organism. We characterized the corresponding regulatory network by comparative transcriptomics and regulon mining as an initial screening tool. Subsequent in-depth transcriptional profiling was applied to define the inducer specificity of each identified cell envelope stress sensor. A total of three TCS and seven ECF sigma factors were shown to be induced by cell envelope stress in B. licheniformis. We noted a number of significant differences, indicative of a regulatory divergence between the two Bacillus species, in addition to the expected overlap in the respective responses.

Adaptation, Physiological↗

Genomic transcriptional profiling of the developmental cycle of Chlamydia trachomatis.

Chlamydia trachomatis is one of the most common bacterial pathogens and is the etiological agent of debilitating sexually transmitted and ocular diseases in humans. The organism is an obligate intracellular prokaryote characterized by a highly specialized biphasic developmental cycle. We have performed genomic transcriptional analysis of the chlamydial developmental cycle. This approach has led to the identification of a small subset of genes that control the primary (immediate-early genes) and secondary (late genes) differentiation stages of the cycle. Immediate-early gene products initiate bacterial metabolism and potentially modify the bacterial phagosome to escape fusion with lysosomes. One immediate early gene (CT147) is a homolog of the human early endosomal antigen-1 that is localized to the chlamydial phagosome; suggesting a functional role for CT147 in establishing the parasitophorous vacuole in a nonfusogenic pathway. Late gene products terminate bacterial cell division and constitute structural components and remodeling activities involved in the formation of the highly disulfide cross-linked outer-membrane complex that functions in attachment and invasion of new host cells. Many of the genes expressed during the immediate-early and late differentiation stages are Chlamydia-specific and have evolutionary origins in eukaryotic lineages.

Bacterial Outer Membrane Proteins↗

Genome-wide profile of oxidoreductases in viruses, prokaryotes, and eukaryotes.

Enzymes that utilize nicotinamide adenine dinucleotide (NAD) or its 2'-phosphate derivative (NADP) are found throughout the kingdoms of life. These enzymes are fundamental to many biochemical pathways, including central intermediary metabolism and mechanisms for cell survival and defense. The complete genomes of 25 organisms representing bacteria, protists, fungi, plants, and animals, and 811 viruses, were mined to identify and classify NAD(P)-dependent enzymes. An average of 3.4% of the proteins in these genomes was categorized as NAD(P)-utilizing proteins, with highest prevalence in the medium-chain oxidoreductase and short-chain oxidoreductase families. In general, the distribution of these enzymes by oxidoreductase family was correlated to the number of different catalytic mechanisms in each family. Organisms with smaller genomes encoded a larger proportion of NAD(P)-dependent enzymes in their proteome (approximately 6%) as compared to the larger genomes of eukaryotes (approximately 3%). Among viruses, those with large, double-strand DNA genomes were shown to encode oxidoreductases. Gram-positive and gram-negative bacteria showed some differences in the distribution of NAD(P)-dependent proteins. Several organisms such as M. tuberculosis, P. falciparum, and A. thaliana showed unique distributions of oxidoreductases corresponding to some phenotypic features.

Animals↗

Population genomics in Sardinia: a novel approach to hunt for genomic combinations underlying complex traits and diseases.

The availability of highly polymorphic markers permits testing whether complex traits and diseases result from genomic interactions between nonallelic normal variants at separate loci. Such variants may be identified by deviations from the expected distributions of alleles at a high number of polymorphic loci, when individuals with the phenotype of interest are compared to normal controls of the same breeding unit, provided that both groups share the same remote ancestry and had no ancestors in common for the last three to four generations. The circumstances needed for such studies are ideally met on the island of Sardinia. The recurrent finding of the same type of association in separate breeding units between the phenotype of interest and a given genotype should allow a distinction between true genetic identity by descent and randomly occurring identities, as these will be obviously different in separate breeding units. The availability of several breeding units located in sharply different ecological environments will permit assessment of the role of nature/nurture factors in the degree of manifestation of each newly discovered genotype/phenotype association. A pilot study to evaluate the proposed strategy has been carried out in the Sardinian village of Carloforte, a community of about 8,000 individuals who have remained genetically homogeneous. Fifty-five control samples have been genotyped with six tetranucleotide microsatellites and with a subset of the 400 markers contained in the ABI PRISM linkage mapping panel, version 2. The allele frequencies for these microsatellite markers have been determined for these 55 individuals and compared to those from a random sampling of subsets of these 55 persons. For the six tetranucleotide microsatellites, a subset of as few as 20 people displayed the same allele frequency distributions as observed with the original 55 unrelated individuals. In conclusion, when samples are chosen from the same breeding unit, the number of individuals sufficient to draw the genomic profile of an isolated population can be relatively small. Likewise, the number of probands with the phenotype of interest can be even smaller when they are ascertained with the same genealogical criteria as the normal controls. By comparing the genomic profile of the probands to a fraction of the control samples within each of several separate breeding units of common remote ancestry, the search for genotype/phenotype association for mono- and multifactorial traits and diseases should be simplified and yield unequivocal results.

Aged↗

Nucleic acid-based analyses of non-group A rotaviruses.

Simple genome profile studies on polyacrylamide gels allow all non-group A rotaviruses isolated so far to be recognized by the absence of the tight triplet (7-9) of RNA segments seen in all group A viruses. However, reliance solely on genome profile studies for rotavirus grouping can be misleading and, for virus group definition, additional corroborating nucleic acid and serological studies are essential. Terminal fingerprint analysis was the first generation of nucleic acid-based assays that allowed discrimination between the various rotavirus groups. By means of this technique the clear definition of five rotavirus groups (A-E), correlating exactly with those found by a serological assay, has been possible, with preliminary evidence for at least two additional groups. The technical sophistication of fingerprinting techniques prevents their widespread use in epidemiological studies; the development of a second generation of nucleic acid-based assays is therefore under way. These employ molecularly cloned cDNA probes to the genomes of non-group A viruses which can be widely distributed for use in 'dot-blot' screening of faecal samples and, if expressed as protein in Escherichia coli, should provide a ready source of viral antigen for use in surveying viral prevalence through the screening of serum antibody levels.

DNA↗

Array comparative genomic hybridization profiling of first-trimester spontaneous abortions that fail to grow in vitro.

OBJECTIVES: Cytogenetic analysis of spontaneous abortion samples can be limited by culture failure. Failure to grow in vitro has traditionally been suspected to be due to in vivo death of tissue associated with spontaneous abortion (SAB) or simply technical factors of growth in culture. METHOD: We used array comparative genomic hybridization (array CGH) to investigate chromosomal imbalances in products of conception that failed to grow in vitro. RESULTS: Our data on 26 cases of SABs that failed to grow in culture are compared and contrasted with published data on cytogenetic findings following in vitro culture. The results revealed abnormalities uncommonly seen by classic cytogenetic methods. These abnormalities include high rates of double aneuploidy and autosomal monosomy. The data taken together suggest that classic cytogenetics of spontaneous abortion may yield normal karyotypes or selected abnormal karyotypes that permit cell proliferation in vitro while Array CGH detects other abnormalities. CONCLUSION: Array CGH is becoming an important clinical assay for unbalanced chromosome abnormalities whether cells grow in culture or not and in cases of analysis on one or few cells.

Abortion, Spontaneous↗

Genome-wide profiling of gene amplification and deletion in cancer.

Accumulations of genetic changes in somatic cells induce phenotypic transformations leading to cancer. Among these genetic changes, gene amplification and deletion are most frequently observed in several kinds of cancers. Amplification of oncogene and/or deletion of tumor suppressor gene, together with dysfunction of the gene by point mutation, are the main causes of cancer. Genome-wide analysis of amplification and deletion of genes in cancers is basic to resolving the mechanisms of carcinogenesis. Comparative genomic hybridization (CGH) developed in 1992 has been utilized to identify DNA copy number abnormalities in various kind of cancers and several reports have shown its usefulness in screening of the genes involved in carcinogenesis, and also in the identification of prognostic factors in cancer. We have shown that 1q23 gain is associated with neuroblastomas that are resistant to aggressive treatment, and have poor prognosis, and 1q and 13q gains are possibly related to drug resistance in ovarian cancers. Recently, the "rough draft" of the human genome was reported and we are ready to utilize the vast information on genomic sequences in cancer research. Moreover, microarray technology enables us to analyze more than ten thousand genes at a time and revealed genetic abnormalities in cancers at a genome-wide level. By combination of microarray and CGH, a powerful screening method for oncogenes and tumor suppressor genes in cancers, called array-CGH, has been developed by several groups. In this article, we overview these genome-wide analytical methods, CGH and array-CGH, and discuss their potential in molecular characterization of cancers.

Gene Amplification↗

Genomic and proteomic profiles of heart disease.

Genomics and proteomics are becoming powerful tools for profiling diseased states. The human genome is estimated to encode 30,000 to 40,000 genes, generating more than 100,000 functionally distinct proteins. Microarray data are available for multiple models of heart disease as well as for diseased and failing human hearts. Similarly, two-dimensional gel data banks of normal and diseased myocardium from multiple species are published and are available on the Internet. The combined technologies are beginning to provide new insights into the causes and pathways of cardiac dysfunction. This article reviews the novel findings that have been acquired from genomic and proteomic screens of diseased hearts in animal models and humans.

Animals↗

Small cell bladder carcinoma with a high tumor mutational burden responding to sequential cisplatin-etoposide and pembrolizumab: a case report.

Small cell carcinoma of the urinary bladder (SCCB) is a rare and aggressive malignancy with limited treatment options and a poor prognosis. We present the case of a 63-year-old man who was initially diagnosed to have non-metastatic high-grade non-muscle invasive urothelial carcinoma with sarcomatoid subtype and later developed bone metastases. A bone biopsy confirmed small cell carcinoma, and retrospective review of the original tumor revealed mixed histology comprising small cell, sarcomatoid-like, and conventional urothelial carcinoma components. The patient was treated with six cycles of cisplatin and etoposide, during which genomic profiling identified a high tumor mutational burden (22 mutations/megabase). Based on this finding, pembrolizumab was administered sequentially as monotherapy. The patient achieved a complete response that lasted for more than 1 year, but subsequently developed lymph node metastases and recurrences in bone. This case highlights the role of genomic profiling test for clinical decision-making as tumor mutational burden predicts the efficacy of immune checkpoint inhibitor therapy in SCCB. This case also underscores the urgent need for novel treatment approaches for SCCB.

Case report↗

Whole-genome expression profiling defines the HrpL regulon of Pseudomonas syringae pv. tomato DC3000, allows de novo reconstruction of the Hrp cis clement, and identifies novel coregulated genes.

Pseudomonas syringae pv. tomato DC3000 is a model pathogen of tomato and Arabidopsis that uses a hypersensitive response and pathogenicity (Hrp) type III secretion system (T3SS) to deliver virulence effector proteins into host cells. Expression of the Hrp system and many effector genes is activated by the HrpL alternative sigma factor. Here, an open reading frame-specific whole-genome microarray was constructed for DC3000 and used to comprehensively identify genes that are differentially expressed in wild-type and deltahrpL strains. Among the genes whose differential regulation was statistically significant, 119 were upregulated and 76 were downregulated in the wild-type compared with the deltahrpL strain. Hierarchical clustering revealed a subset of eight genes that were upregulated particularly rapidly. Gibbs sampling of regions upstream of HrpL-activated operons revealed the Hrp promoter as the only identifiable regulatory motif and supported an iterative refinement involving real-time polymerase chain reaction testing of additional HrpL-activated genes and refinements in a hidden Markov model that can be used to predict Hrp promoters in P. syringae strains. This iterative bioinformatic-experimental approach to a comprehensive analysis of the HrpL regulon revealed a mix of genes controlled by HrpL, including those encoding most type III effectors, twin-arginine transport (TAT) substrates, other regulatory proteins, and proteins involved in the synthesis or metabolism of phytohormones, phytotoxins, and myo-inositol. This analysis provides an extensively verified, robust method for predicting Hrp promoters in P. syringae genomes, and it supports subsequent identification of effectors and other factors that likely are important to the host-specific virulence of P. syringae.

Bacterial Proteins↗

Futibatinib after non-covalent FGFR inhibitors in FGFR2-rearranged intrahepatic cholangiocarcinoma: clinical activity and resistance patterns.

PURPOSE: The optimal sequencing of non-covalent and covalent FGFR inhibitors in FGFR2-rearranged intrahepatic cholangiocarcinoma (iCCA) remains undefined. Futibatinib, an irreversible FGFR1-4 inhibitor, may retain activity in the setting of acquired resistance to non-covalent FGFR inhibitors, but data on the patterns of acquired alterations are limited. METHODS: We conducted a retrospective multicenter study across three European centers including patients with advanced FGFR2-rearranged iCCA treated with futibatinib after progression on non-covalent FGFR inhibitors. Clinical outcomes and safety were evaluated. Available genomic profiling at progression was analyzed to characterize resistance mechanisms and their association with outcomes. RESULTS: Sixteen patients were included. Median progression-free survival (mPFS) with prior non-covalent FGFR inhibitors was 10.2 months (95% CI 7.0-15.5), with an objective response rate (ORR) of 60.0%. Among patients with post-progression genomic profiling (n = 11), all harbored FGFR2 resistance mutations, with polyclonal alterations (≥2) in 45.5%. A higher burden of FGFR2 mutations and the presence of co-alterations were associated with shorter mPFS on non-covalent inhibitors. Futibatinib was administered at a median of fourth-line therapy. ORR was 31.3% and disease control rate was 50.0%. Median PFS and overall survival were 4.5 months (95% CI 2.0-9.1) and 9.9 months (95% CI 5.7-not reached), respectively. Notably, outcomes with futibatinib were independent of the number of acquired FGFR2 resistance mutations, and the adverse impact of co-alterations appeared attenuated. Safety was consistent with the known profile. CONCLUSIONS: Futibatinib demonstrates clinically meaningful activity after progression on non-covalent FGFR inhibitors, supporting its use in FGFR2-rearranged iCCA, including in the post-non-covalent inhibitor setting. The distinct resistance patterns provide a biological rationale for the continued efficacy of covalent FGFR inhibition. Prospective studies incorporating longitudinal molecular profiling are needed to optimize treatment sequencing.

Drug resistance↗

Whole-genome transcription profiling reveals genes up-regulated by growth on fucose in the human gut bacterium "Roseburia inulinivorans".

"Roseburia inulinivorans" is an anaerobic polysaccharide-utilizing firmicute bacterium from the human colon that was identified as a producer of butyric acid during growth on glucose, starch, or inulin. R. inulinivorans A2-194 is also able to grow on the host-derived sugar fucose, following a lag period, producing propionate and propanol as additional fermentation products. A shotgun genomic microarray was constructed and used to investigate the switch in gene expression that is involved in changing from glucose to fucose utilization. This revealed a set of genes coding for fucose utilization, propanediol utilization, and the formation of propionate and propanol that are up-regulated during growth on fucose. These include homologues of genes that are implicated in polyhedral body formation in Salmonella enterica. Dehydration of the intermediate 1,2-propanediol involves an enzyme belonging to the new B12-independent glycerol dehydratase family, in contrast to S. enterica, which relies on a B12-dependent enzyme. A typical gram-positive agr-type quorum-sensing system was also up-regulated in R. inulinivorans during growth on fucose. Despite the lack of genome sequence information for this commensal bacterium, microarray analysis has provided a powerful tool for obtaining new information on its metabolic capabilities.

Bacteria, Anaerobic↗

Cloning, expression profile, and genomic organization of the mouse STAP/A170 gene.

The preferential screening of cDNA libraries derived from the mouse osteoblastic cell line MC3T3-E1 has yielded a cDNA clone encoding a 442-amino-acid protein designated STAP (signal transduction and adaptor protein), which contains several motifs shared among transcription factors and adaptors such as a Zn-finger like motif, a proline-rich domain, and a PEST sequence. The amino acid sequence homology search also reveals that STAP is identical to a mouse oxidative stress protein, A170, and has 90% homology with a human p62 protein that binds to the tyrosine kinase p56(lck) SH2 domain. Northern blot analysis indicated a broad expression profile of STAP mRNA in various tissues and cell lines. In MC3T3-E1 cells, STAP mRNA was induced by treatment with TGF-beta, but not with BMP-2 or GDF-5. Analysis of the mouse STAP gene isolated from the genomic library revealed that the STAP gene spans a region of over 11 kb and comprises eight exons. The transcription start site was identified by primer extension analysis to be located 35 bp upstream from the translation initiation site. Sequencing analysis of the 5' flanking region of the STAP gene revealed multiple consensus motifs/sequences for several DNA binding transcription factors. The STAP gene had a TATA box, but no CCAAT box. Potential Sp1, AP-1, NF-E2, MyoD, and NF-kappaB binding sites were found in the 5' flanking region (1.4 kb) of the STAP gene.

3T3 Cells↗

The use of DNA microarrays to assess clinical samples: the transition from bedside to bench to bedside.

The advent of gene array technology brings the ability to classify disease states to the molecular level by examining changes in all mRNAs expressed in cells or tissues. Comparing changes in gene expression patterns between normal and diseased cells and/or tissues has elucidated unique subsets of genes identifiable to a specific disease. Already, new subclassifications of specific cancers have been discovered, belying that genomic profiling can uniquely distinguish a specific disease state and tissue of origin. This technology bestows the ability to examine global changes occurring in a cell or tissue(s), thereby allowing the elucidation of alterations in dysregulated biological, biochemical, and molecular events leading to disease states such as diabetes, hypertension, infertility, obesity, osteoporosis, and atherosclerosis. Furthermore, genomic profiling will lead to new molecular targets for the development of drug therapeutics. Futuristically, one could envision personalized patient therapies based upon identification of specific aberrant signaling pathways that can be targeted for drug therapy.

Androgens↗