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PubMed2026

Meta-Merging the Transcriptomes of Gastric Tumors Redefines the Connections among Molecular and Clinical Subtypes.

INTRODUCTION: The availability of a large number of cancer expression profiles presents an excellent opportunity to re-investigate various biological and clinical questions. While several expression profiles have been established for different cancers, merging them may provide a more powerful platform for extensively extrapolating molecular and clinical features across multiple cohorts. MATERIALS AND METHODS: In this study, five gastric tumor expression profiles from the Gene Expression Omnibus [GEO] and one in-house cohort comprising a total of 1,060 samples were merged. The batch effect was removed using non-parametric ComBat analysis, and the seamless merging of datasets was confirmed through various parameters. RESULTS: Extrapolation of ACRG [Asian Cancer Research Group] and TCGA [The Cancer Genome Atlas] molecular subtypes in the merged cohort of 1,060 gastric tumors revealed nine distinct clusters. Notably, the following patterns were observed: [i] mutual exclusivity between Epithelial to Mesenchymal Transition [EMT] and Microsatellite Instability [MSI] subtypes in 90% of tumors; [ii] overlapping occurrence of EMT and MSI subtypes in the remaining tumors; [iii] overlap between MSI and Epstein-Barr Virus [EBV] subtype tumors; [iv] both commonalities and differences between EMT and Genomically Stable [GS] subtypes; and [v] an association between EBV positivity and PI3K mutation. CONCLUSION: The current study demonstrates that compiling a larger expression profile is valuable for revisiting the molecular features and epidemiology associated with molecular subtypes, thereby aiding in the development of novel diagnostics and targeted therapeutics.

Humans↗

PubMed2001

The H1 double-stranded RNA genome of Ustilago maydis virus-H1 encodes a polyprotein that contains structural motifs for capsid polypeptide, papain-like protease, and RNA-dependent RNA polymerase.

The Ustilago maydis viral (UmV) genome consists of three distinct size groups of double-stranded RNA (dsRNA) segments: H (heavy), M (medium), and L (light). The H segments have been suggested to encode all essential viral proteins, but without any molecular evidences. As a preliminary step to understand viral genomic organization and the molecular mechanism governing gene expression in UmV, we determined the complete nucleotide sequence of the H1 dsRNA genome in P1 viral killer subtype. The H1 dsRNA genome (designated UmV-H1) contained a single open reading frame that encodes a polyprotein of 1820 residues, which is predicted to be autocatalytically processed by a viral papain-like protease to generate viral proteins. The amino-terminal region is the capsid polypeptide with a predicted molecular mass of 79.9 kDa. The carboxy-terminal region is the RNA-dependent RNA polymerase (RDRP) that has a high sequence homology to those of the totiviruses. The H2 dsRNA also encodes a distinct RDRP, suggesting that UmV is a complex virus system like the Saccharomyces cerevisiae viruses ScV-L1 and -La.

Amino Acid Sequence↗

PubMed2005

Amplification and cloning of near full-length HIV-2 genomes.

The genomes of human immunodeficiency virus type 2 (HIV-2), like those of HIV-1, are not only extremely variable but are also highly recombinogenic. Determination of subtypes based on partial genomes cannot predict the subtype classification of other regions of the genome owing to the frequent occurrence of recombinant genomes among subtypes. To fully understand the genetic variation and evolution of HIV-2s, full-length viral genomes need to be obtained for genetic analysis. Full-length HIV-2 genomes can also be used as infectious clones to study viral biological characteristics and as reference sequences for phylogenetic analysis. More important, all genes in the obtained genomes can be cloned into expression vectors to produce proteins that can be used as antigens for diagnostic reagents or as immunogens for vaccine development. The long-range polymerase chain reaction technique has recently become a more preferred method than the lambda phage cloning method to obtain near-full-length HIV-2 genomes.

Cloning, Molecular↗

PubMed2026

Clinical outcomes and genomic features of uncommon EGFR exon 19 deletion subtypes in osimertinib-treated non-small cell lung cancer.

BACKGROUND: Epidermal growth factor receptor (EGFR) exon 19 deletion subtypes may be associated with differential survival outcomes following EGFR-tyrosine kinase inhibitor treatment. However, evidence remains scarce, particularly regarding osimertinib, and the underlying biological mechanisms are poorly understood. We aimed to compare survival outcomes among EGFR exon 19 deletion subtypes in patients with non-small cell lung cancer (NSCLC) treated with osimertinib. METHODS: In this multicenter retrospective study, patients with NSCLC were stratified according to exon 19 deletion subtypes. Whole-exome sequencing data from the American Association for Cancer Research Genomics Evidence Neoplasia Information Exchange registry and Memorial Sloan Kettering Clinicogenomic Harmonized Oncologic Real-World Dataset were analyzed to investigate co-occurring genomic alterations. RESULTS: Overall, 111 patients with advanced EGFR exon 19 deletion-positive NSCLC were analyzed and 86.5% received osimertinib as first-line therapy. Patients with non-E746_A750del (n = 25) had shorter progression-free survival (PFS) than those with E746_A750del (n = 86) (median: 14.3 vs. 20.6 months; p < 0.05). Among non-E746_A750del subtypes, L747_A750delinsP (n = 4) had a particularly poor prognosis, with significantly worse survival than those with E746_A750del (median PFS: 3.5 vs. 20.6 months; p < 0.001, and median overall survival: 11.8 vs. 48.5 months; p < 0.001). In public database analyses, non-E746_A750del had a higher rate of RBM10 co-mutations, whereas L747_A750delinsP was characterized by frequent CDKN2A/B homozygous deletions and MYC amplifications. CONCLUSIONS: Non-E746_A750del was associated with poorer outcomes, with L747_A750delinsP potentially being a high-risk subtype. Differences in co-occurring genomic alterations may contribute to the prognostic heterogeneity among exon 19 deletion subtypes.

Humans↗

PubMed2026

Sparse Logistic Regression on Genomic Data for Prediction of Tumour Pathological Subtype.

The correct prediction of tumour subtype is critical for the treatment of cancer patients to maximise the chance of survival. The patients' genomic information, such as copy number alterations (CNA) profile, has increasingly become an important factor in the prediction to supplement the traditional pathological subtyping. The incorporation of the CNA information in a prediction model, such as logistic regression, faces two major statistical challenges: first, how to estimate the model parameters in the thousands and, second, how to deal with the correlation of CNA between genomic regions. To address them, we propose a sparse logistic regression model with random effects where some of its parameters are estimated to zero while the other parameters are non-zero. In effect, a variable selection is embedded in the modelling. To deal with the correlation of CNA across genomic regions, we extend further the model to incorporate an additional penalty in the corresponding likelihood function in the logistic regression. The results show that we can identify selected genomic regions that are informative to distinguish different tumour subtypes, while giving a good prediction ability. We illustrate the methodology using CNA dataset from a lung cancer cohort.

Journal Article↗

PubMed1998

Full genome sequences of human immunodeficiency virus type 1 subtypes G and A/G intersubtype recombinants.

Multiple genetic subtypes and intersubtype recombinant strains have been identified among isolates of HIV-1. The greatest diversity of strains has been recovered from Central Africa, where mixtures of subtypes and recombinant forms have been recovered. However, many of the HIV-1 subtypes and recombinants have been characterized by partial rather than full-length genome sequencing. Here we report the first two virtually full-length genome sequences from HIV-1 subtype G, isolated in Sweden and Finland but originating in Congo and Kenya, and from two Djibouti isolates sharing the A/G recombinant structure of Nigerian isolate, IbNG. By comparison with reference sequences of other subtypes, it appears that the subtype G strains are largely nonrecombinant, while the Djibouti strains show alternating segments from subtypes A and G. In the cytoplasmic domain of the gp41 protein of the Djibouti viruses the E, G, and IbNG strains form a single cluster, separate from subtype A, clouding the subtype origin of these particular segments. Within the resolution of current technology, the structure of the Djibouti strains is identical to that of IbNG, establishing for the first time the geographic spread of this recombinant in Africa. The geographic spread of the IbNG-like strains suggests that, like the subtype E recombinants, these should be given a specific name to facilitate future identification and tracking; the name "IbNG subtype" is proposed.

Base Sequence↗

PubMed2002

Amplification of the effects of drug resistance mutations by background polymorphisms in HIV-1 protease from African subtypes.

The vast majority of HIV-1 infections worldwide are caused by the C and A viral subtypes rather than the B subtype prevalent in the United States and Western Europe. Genomic differences between subtypes give rise to sequence variations in the encoded proteins, including those identified as targets for antiretroviral therapies. In the case of the HIV-1 protease, we reported earlier [Velazquez-Campoy et al. (2001) Proc. Natl. Acad. Sci. U.S.A. 98, 6062-6067] that proteases from the C and A subtypes exhibit a higher biochemical fitness in the presence of widely prescribed protease inhibitors. In this paper we present a complete thermodynamic dissection of the differences between proteases from different subtypes and the effects of the V82F/I84V drug-resistant mutation within the framework of the B, C, and A subtypes. These studies involved four inhibitors in clinical use (indinavir, saquinavir, ritonavir, and nelfinavir) and a second-generation protease inhibitor (KNI-764). Naturally occurring amino acid polymorphisms found in proteases from the C and A subtypes lower the binding affinities of existing clinical inhibitors by factors ranging between 2 and 7.5 which by themselves are not enough to cause drug resistance. The preexisting lower affinity in the C and A subtypes, however, significantly amplifies the effects of the drug-resistant mutation. Relative to the wild-type B subtype protease, the V82F/I84V drug-resistant mutation within the C and A subtypes lowers the binding affinity of inhibitors by factors ranging between 40 and 3000. When the enzyme kinetic properties (k(cat) and K(m)) are included in the analysis, the biochemical fitness of the C and A subtype drug-resistant mutants can be up to 1000-fold higher than that of the wild-type B subtype protease in the presence of the studied inhibitors. From a thermodynamic standpoint, the combined effects of the drug-resistant mutations and the natural amino acid polymorphisms on the Gibbs energy are additive and involve significant alterations in the enthalpy and entropy changes associated with inhibitor binding. At the biochemical level, the combined effects of naturally existing polymorphisms and drug-resistant mutations might have important consequences on the long-term viability of current HIV-1 protease inhibitors.

Africa↗

PubMed2001

Catalytic efficiency and vitality of HIV-1 proteases from African viral subtypes.

The vast majority of HIV-1 infections in Africa are caused by the A and C viral subtypes rather than the B subtype prevalent in the United States and Western Europe. Genomic differences between subtypes give rise to sequence variations in the encoded proteins, including the HIV-1 protease. Because some amino acid polymorphisms occur at sites that have been associated with drug resistance in the B subtype, it is important to assess the effectiveness of protease inhibitors that have been developed against different subtypes. Here we report the enzymatic characterization of HIV-1 proteases with sequences found in drug-naive Ugandan adults. The A protease used in these studies differs in seven positions (I13V/E35D/M36I/R41K/R57K/H69K/L89M) in relation to the consensus B subtype protease. Another protease containing a subset of these amino acid polymorphisms (M36I/R41K/H69K/L89M), which are found in subtype C and other HIV subtypes, also was studied. Both proteases were found to have similar catalytic constants, k(cat), as the B subtype. The C subtype protease displayed lower K(m) values against two different substrates resulting in a higher (2.4-fold) catalytic efficiency than the B subtype protease. Indinavir, ritonavir, saquinavir, and nelfinavir inhibit the A and C subtype proteases with 2.5-7-fold and 2-4.5-fold weaker K(i)s than the B subtype. When all factors are taken into consideration it is found that the C subtype protease has the highest vitality (4-11 higher than the B subtype) whereas the A subtype protease exhibits values ranging between 1.5 and 5. These results point to a higher biochemical fitness of the A and C proteases in the presence of existing inhibitors.

Adult↗

PubMed1999

[Genetic diversity of HIV infection worldwide and its consequences].

Phylogenetic study of HIV-1 strains from different geographical locations has revealed the existence of three separate groups that have been named M, N, and O. Most strains involved in the pandemia belong to group M which contains several subtypes. Nearly 20 p. 100 of isolates in group M are recombinant with genomic components from different subtypes. Some mosaic virus are one-of-a-kind or limited to small transmission groups while others are major players in the worldwide AIDS epidemic. They are currently called circulating recombinant forms (CRFs). Since subtypes or CRFs must be similar over the whole genome, only 9 subtypes are possible within group M (A, B, C, D, F, G, H, J and K). Viruses E and I in the envelope are recombinant. Subtyping is a powerful molecular tool for monitoring the evolution of the HIV-1 epidemic. Overall the predominant viral forms in the world are subtypes A and C followed by recombinant CRF01-AE (formerly subtype E) and CRF02-AG (identical to the IBNG prototype strain in Nigeria) and subtype B. The highest degree of genetic diversity in HIV-1 is observed in Africa where all subtypes and groups can be observed. The geographic distribution of subtypes is subject to constant change. Recombinant forms of the virus will continue to appear as long as the different subtypes of HIV-1 continue to circulate between continents and recombination continues to occur.

Acquired Immunodeficiency Syndrome↗

PubMed2005

Circulation of novel HIV type 1 A, B/C, and F subtypes in Argentina.

The Argentine HIV-1 epidemic is considered to be represented mainly by subtype B and diverse B/F recombinants, with apparent absence of pure subtype F. In this study we describe three novel HIV-1 variants isolated from four infants born in different and distant provinces of Argentina. Partial analysis of different gene fragments spanning 18.5-40.8% of the HIV-1 complete genome revealed two subtype A HIV-1 strains in siblings, a B/C recombinant with a novel mosaic structure, and a putative subtype F. Characteristic patterns of genomic and amino acid sequences of the newly reported subtype F isolate suggest a closer genetic relationship to Argentine B/F recombinants than any other subtype F strain described so far, while the A and B/C subtypes found correspond to unusual genotypes in Argentina. Understanding the origin, diversity, and spread of HIV-1 strains worldwide will be necessary for the development of an effective vaccine approach.

Amino Acid Sequence↗

PubMed2006

Genomic instability and prognosis in breast carcinomas.

BACKGROUND: We recently reported that DNA content of breast adenocarcinomas, cytometrically assessed by diploid (D), tetraploid (T), and aneuploid (A) categories, can be further divided into genomically stable and unstable subtypes by means of the stemline scatter index (SSI). The aim of the present study was to survey the clinical correlates and the prognostic value of the SSI in a consecutive series of 890 breast cancer patients. RESULTS: Genomically stable subtype had a significantly better survival compared with the unstable subtype within each ploidy category: D (P = 0.04), T (P = 0.008), and A (P = 0.004). By contrast, no statistically significant difference in survival was observed between the D, T, and A categories within the stable (P = 0.23) and unstable subtypes (P = 0.12). Among A tumors, the unstable subtype tended to be larger, more frequently estrogen- and progesterone-receptor negative, and to be of higher grade compared with the stable subtype. Stable D tumors tended to have lower grade than the unstable subtype, but among the D and T tumors, genomic instability was not associated with receptor status. Within the Elston grade 3, lymph node-positive or estrogen receptor-positive subgroups, patients with stable tumors had significantly better survival compared with unstable tumors (P = 0.01, 0.002, and 7.2E-5, respectively). CONCLUSIONS: The SSI contributes supplementary biological and clinical information in addition to ploidy information alone. Objective classification of breast adenocarcinomas into stable and unstable subtypes is a useful prognostic indicator independent of established clinical factors.

Adult↗

PubMed1989

Genome sequence of tick-borne encephalitis virus (Western subtype) and comparative analysis of nonstructural proteins with other flaviviruses.

The genome sequence of tick-borne encephalitis (TBE) virus (Western subtype vaccine strain Neudoerfl) was determined. This extends the previously published sequence of the structural proteins to the nonstructural protein region and noncoding sequences at the 5'- and 3'-termini. The amino-termini of the individual proteins were assigned by comparison with other flavivirus sequences. Amino acid homology calculations between TBE virus and mosquito-borne flaviviruses were performed for all nonstructural proteins. An evolutionary tree based on protein NS1 is presented that reveals the molecular basis of relationships among flaviviruses. Tick-borne and mosquito-borne flaviviruses share a common hydrophilicity profile and also other features of their primary sequences, such as the presumably functional Gly-Asp-Asp sequence element within protein NS5. Other characteristics, such as the potential N-glycosylation sites of protein NS1 and a potential proteolytic cleavage site within protein NS4B, are conserved within the mosquito-borne group, but differ in the TBE virus sequence.

Amino Acid Sequence↗

PubMed2005

Evolutionary conservation of the structural, pharmacological, and genomic characteristics of the melanocortin receptor subtypes.

We have cloned melanocortin receptors (MCRs) from several species of fish. The MC4R and MC5R subtypes arose early in vertebrate evolution and their primary structure is remarkably conserved. Expression and pharmacological characterization of the MCRs in fish has revealed that they bind and respond to melanocortin peptides with high potency. Detailed characterization of the binding properties of the different subtypes suggests that MCRs in early vertebrates had preference for adrenocorticotropic hormone (ACTH) peptides, while the high sensitivity for the shorter proopiomelanocortin (POMC) products, such as the alpha-, beta-, and gamma-melanocyte-stimulating hormone (MSH), has appeared later, perhaps as the MCR subtypes gained more specialized functions. The MCR repertoire shows in general high similarities in their primary structures, while they are however not similar in terms of functional roles. The MCRs serve therefore as an interesting model family to understand the molecular mechanisms of how functions of the genes can diverge during evolution. In this review, we provide an overview of our recent studies on the cloning, expression, pharmacology, 3D modeling, and genomic studies of the MCRs in non-mammalian species.

Amino Acid Sequence↗

PubMed2026

Genomic wastewater surveillance of human and animal influenza A viruses in California during the 2024-2025 flu season.

BACKGROUND: Wastewater genomic surveillance provides an opportunity to detect human and animal influenza A virus (IAV). We aimed to implement an IAV genomic surveillance framework agnostic to subtype, which enables recovery of IAV from multiple hosts and estimation of proportions across subtypes. METHODS: We conducted IAV genomic surveillance in wastewater during the 2024-2025 flu season at multiple sites in California and compared these data with available human clinical IAV sequences and test positivity. We applied a custom whole-genome, multi-host IAV probe enrichment panel and adapted our custom expectation-maximization (EM) algorithm to deconvolute IAV mixtures in wastewater and infer subtype relative abundances. Absolute IAV concentrations were quantified using RT-PCR-based assays. H5N1 wastewater and clinical sequences were further characterized by constructing a whole-genome maximum-likelihood phylogenetic tree. Finally, we performed variant analysis to examine amino acid substitutions detected in wastewater. FINDINGS: Our IAV probe enrichment method and EM algorithm successfully enriched all eight segments of three circulating IAV subtypes and accurately estimated subclade relative abundances for mixed IAV samples. Seasonal human H1N1pdm09 and H3N2 were detected throughout the study period from both wastewater and clinical sequencing data, with H1N1 subclades 6B.1A.5a.2a.1 and 6B.1A.5a.2a co-circulating, and H3N2 dominated by subclade 3C.2a1b.2a.2a.3a.1. Wastewater surveillance consistently detected H5N1 clade 2.3.4.4b across three monitored wastewater sites, while clinical H5N1 detections, from anywhere in CA, were sporadic and rare. Whole-genome phylogenetic analysis revealed that wastewater H5N1 sequences clustered with reference sequences associated with dairy cow and avian infections, while all human clinical H5N1 sequences clustered exclusively with reference sequences associated with dairy cow infections. Amino acid substitutions were identified across viral segments, and no mutations associated with mammalian adaptation were observed from wastewater samples. INTERPRETATION: When IAV concentrations were dominated by seasonal human subtypes rather than H5N1, subtype patterns aligned between wastewater and clinical data. While sequencing IAV in wastewater was unable to distinguish if H5N1 detections were due to human or animal infections, it was able to provide clade-level information about H5N1 found in wastewater that could be useful in the future. Wastewater genomic surveillance can complement clinical surveillance, increasing ability to detect all circulating IAV subtypes and enhancing public health preparedness from a One Health perspective.

Journal Article↗

PubMed2002

[Construction and biological activity assessment of core mutants of hepatitis B virus adr subtype].

OBJECTIVE: To construct the core mutant (L97 and V60) plasmids of hepatitis B virus (HBV) and assess their biological activity. METHODS: Site-directed mutagenesis was performed to induce specific core point mutations in HBV adr suhtype 1.2 copy genome plasmid p3.8 II. The plasmids were transfected into HepG2 cells via liposome, and intracellular HBV DNA was analyzed by Southern hybridization, while extracellular HBV antigens (HBsAg and HBeAg) in the culture supernatant were assayed by enzyme-linked immunosorbent assay. RESULTS: Sequence analysis of the constructed mutant plasmids p3.8 L97 and p3.8 V60 demonstrated mutations at 2 189 A C and 2 086 C HBV adr subtype genome core mutant (L97 and V60) plasmids we have constructed possess biological activity.G respectively. These mutant plasmids exhibited HBV DNA replication activity and gene expression in host cells. CONCLUSION: HBV adr subtype genome core mutant (L97 and V60) plasmids we have constructed possess biological activity.

Base Sequence↗

PubMed2006

Superinfection of human immunodeficiency virus type 1 (HIV-1) to cell clone persistently infected with defective virus induces production of highly cytopathogenic HIV-1.

Superinfection with human immunodeficiency virus type 1 (HIV-1) in human subjects, defined as reinfection with a heterologous strain of HIV-1, has become a topic of great interest. To illustrate the significance of this occurrence, we performed HIV-1 superinfection of L-2 cells, which were isolated from MT-4 cells persistently infected with subtype B HIV-1 as a cell clone continuously producing defective HIV-1 particles. L-2 cells carrying provirus with a one-base insertion in the pol protease were superinfected with HIV-1 derived from primary isolates of subtype B or CRF01_AE. The kinetics of the superinfection in L-2 were very slow compared with those of primary infections in MT-4. Interestingly, L-2 shifted after superinfection to become a producer of highly cytopathogenic HIV-1. Molecular characterization revealed that superinfection occurred in only about 10% of the CRF01_AE-superinfected L-2, which carried provirus of both subtypes and produced viral particles containing genomic RNA of both subtypes. Surprisingly, such cytopathogenic HIV-1 showed predominantly the original subtype B phenotype. Thus, the mechanism of the production of cytopathic HIV-1 seemed to be mediated by trans complementation with pol products of superinfected CRF01_AE. These findings suggest the significance of long-lived infected cells as recipients for superinfection that could result in the generation of new HIV-1 variants with high virulence in patients who are off therapy or do not adhere to treatment, and may indicate the need for precautions against such superinfection.

Cell Line↗

PubMed2005

Comparative genomics of the human and Fugu voltage-gated calcium channel alpha1-subunit gene family reveals greater diversity in Fugu.

Extensive search for the orthologs of 10 human voltage-gated calcium channel (VGCC) alpha(1)-subunit genes in the Fugu genome sequence revealed 21 alpha(1)-subunit genes in the compact genome of Fugu. Subtype classification of the identified Fugu alpha(1) orthologs based on phylogenetic analysis, genomic organization and sequence comparison of the most divergent II/III loop and the C-terminal regions of the alpha(1)-subunits indicated extra copies of alpha(1S)-, alpha(1D)-, alpha(1F)-, alpha(1A)-, alpha(1E)-, alpha(1H)- and alpha(1G)-subunit genes. Phylogenetic analysis reveals that this is likely due to fish lineage specific alpha(1)-subunit subtype duplication. Sequence comparison shows that many of the structural features characteristic of VGCC and specific channel subtypes are also present in the Fugu alpha(1)-subunits. All the Fugu alpha(1)-subunits showed similar expression profile to that of the mammalian alpha(1)-subunits except for Fugu alpha(1S), alpha(1A), alpha(1B) and alpha(1H) which have a more widespread tissue distribution. These results indicate that Fugu, a lower vertebrate, has more extensive channel heterogeneity compared to human.

Animals↗

PubMed1999

Methods for subtyping and molecular comparison of human viral genomes.

The development over the past two decades of molecular methods for manipulation of RNA and DNA has afforded molecular virologists the ability to study viral genomes in detail that has heretofore not been possible. There are many molecular techniques now available for typing and subtyping of viruses. The available methods include restriction fragment length polymorphism analysis, Southern blot analysis, oligonucleotide fingerprint analysis, reverse hybridization, DNA enzyme immunoassay, RNase protection analysis, single-strand conformation polymorphism analysis, heteroduplex mobility assay, nucleotide sequencing, and genome segment length polymorphism analysis. The methods have certain advantages and disadvantages which should be considered in their application to specific viruses or for specific purposes. These techniques are likely to become more widely used in the future for epidemiologic studies and for investigations into the pathophysiology of virus infections.

Blotting, Southern↗