E2 Gene Research Articles

GmEID1 modulates light signaling through the Evening Complex to control flowering time and yield in soybean

Soybean (Glycine max) morphogenesis and flowering time are accurately regulated by photoperiod, which determine the yield potential and limit soybean cultivars to a narrow latitudinal range. The E3 and E4 genes, which encode phytochrome A photoreceptors in soybean, promote the expression of the legume-specific flowering repressor E1 to delay floral transition under long-day (LD) conditions. However, the underlying molecular mechanism remains unclear. Here, we show that the diurnal expression pattern of GmEID1 is opposite to that of E1 and targeted mutations in the GmEID1 gene delay soybean flowering regardless of daylength. GmEID1 interacts with J, a key component of circadian Evening Complex (EC), to inhibit E1 transcription. Photoactivated E3/E4 interacts with GmEID1 to inhibit GmEID1-J interaction, promoting J degradation resulting in a negative correlation between daylength and the level of J protein. Notably, targeted mutations in GmEID1 improved soybean adaptability by enhancing yield per plant up to 55.3% compared to WT in field trials performed in a broad latitudinal span of more than 24°. Together, this study reveals a unique mechanism in which E3/E4-GmEID1-EC module controls flowering time and provides an effective strategy to improve soybean adaptability and production for molecular breeding.

TRANSLACOL project: Nodal human papillomavirus tumoral DNA detection by ddPCR for survival prediction in early cervical cancer patients without pelvic lymph node invasion

In early cervical cancer (EEC), 10 to 15% of patients without nodal metastasis (N-) will suffer from recurrences with further similar survival as N+ patients. However, no clinical, imaging or pathological risk-factor is today available to identify them. In the present study, we hypothesized that the N- histologically characterized patients who present a poor prognosis could be patients for whom metastasis are missed by classical procedure. Therefore, we propose to research HPV tumoral DNA (HPVtDNA) in pelvic Sentinel Lymph Nodes (SLN) biopsy using ultrasensitive droplet-based digital PCR (ddPCR) to detect eventual occult metastasis. Sixty HPV16, HPV18 or HPV33 positive EEC N- patients with available SLN were included. In SLN, HPV16 E6, HPV18 E7 and HPV33 E6 gene were respectively detected using ultrasensitive ddPCR technology. Survival data were analysed using Kaplan-Meier-curves and log-rank-test to compare progression-free survival (PFS) and disease-specific survival (DSS) in two groups according to their HPVtDNA status in SLN. More than half (51.7%) of the patients finally showed HPVtDNA positivity in SLN initially diagnosed as negative by histology. Two patients with negative HPVtDNA SLN and 6 with positive HPVtDNA SLN group presented recurrence. Finally, all of the 4 deaths listed in our study occurred in the positive HPVtDNA SLN group. These observations hint that the use of ultrasensitive ddPCR to detect HPVtDNA in SLN could allow the identification of two subgroups of histologically N- patients that may have different prognosis and outcome. To our knowledge, our study is the first one to evaluate the detection of HPVtDNA in SLN in early cervical cancer using ddPCR highlighting its interest as a complementary tool for N- specific early cervical cancer diagnosis.

Extrachromosomal Amplification of Human Papillomavirus Episomes Is a Mechanism of Cervical Carcinogenesis.

Multimers of the HPV genome are generated in cervical tumors replicating as extrachromosomal episomes, which is associated with deletion and rearrangement of the HPV genome and provides a mechanism for oncogenesis without integration.

FDA-APPROVED MOLECULAR TESTS USED TO DEFINE HUMAN PAPILLOMAVIRUS (HPV) INFECTIONS WHICH CAUSE CERVIX CANCER

Human papillomavirus (HPV) is a non-enveloped, commonly sexually transmitted virus with icosahedral symmetry and double-stranded circular DNA. Its genome, which is about 8 kb in size, encodes early genes (E1-8) and two late structural capsid genes (L1 and L2). Among the genes that play a role in viral pathogenesis, L1, E6, and E7 genes frequently exist. The E6 and E7 viral genes have a significant role in apoptosis inhibition, viral spread, development of squamous intraepithelial lesion (SIL), cell immortalization, neoplastic transformation, and invasive cancer.
 Demonstration of the relationship between cervical cancer and HPV infections has led to increased interest in this subject and the classification of some HPV genotypes in the high-risk group (HR-HPV) for cervical cancer. Numerous commercial molecular tests have been developed for the identification of HPV genotypes involving different approaches. HPV molecular tests approved by the US Food and Drug Administration (FDA) include Hybrid Capture® 2 (HC2), Cervista™, cobas®, Aptima®, and BD Onclarity™. This article reviews the methodologies, limitations, and commonalities of five FDA-approved tests. The HC2 and Cervista™ tests use non-PCR-based signal amplification methods, while the cobas® and BD Onclarity™ tests use PCR-based target amplification methods. On the other hand, the Aptima® test uses the mRNA transcriptional mediated amplification (TMA) method.
 Each of these methods used in the diagnosis and follow-up of HPV has its strengths and weaknesses. These HPV molecular tests have high sensitivity and specificity. They are also more automated and repeatable than cytological methods. In addition to these advantages, there are also several limitations. Because of these limitations, molecular tests are no more perfect than cytological tests. This situation shows that these tests should not be used alone in the evaluation of HPV infections and cancer identification. On the contrary, HPV test results should be correlated with cytology or biopsy findings.

Polymorphism of E6 and E7 Genes in Human Papillomavirus Types 31 and 33 in Northeast China.

Persistent infection with human papillomavirus (HPV) types 31 and 33 is an important causative factor for cervical cancer. The E6/E7 genes are key oncogenes involved in the immortalization and transformation of human epithelial cells. Genetic polymorphism may lead to differences in the virus' carcinogenic potential, the immune reaction of the host, and the potencies of vaccines. Few studies on HPV31/33 E6/E7 genetic polymorphism have been carried out. To study the genetic polymorphism of HPV31 and HPV33 E6/E7 genes in northeast China, these genes (HPV31 E6/E7, n = 151; HPV33 E6/E7, n = 136) were sequenced and compared to reference sequences (J04353.1, M12732.1) using BioEdit. Phylogenetic trees were constructed by the neighbor-joining method using MegaX. The diversity of the secondary structure was estimated using the PSIPred server. The positively selected sites were analyzed using PAML4.9. The major histocompatibility complex (MHC) class I and MHCII epitopes were predicted using the ProPred-I server and ProPredserver. B-cell epitopes were predicted using the ABCpred server. In the 151 HPV31E6 sequences, 25 (25/450) single-nucleotide mutations were found, 14 of which were synonymous mutations and 11 were nonsynonymous. In the 151 HPV31E7 sequences, 8 (8/297) nucleotide mutations were found, 3 of which were synonymous mutations and 5 were nonsynonymous. In the 136 HPV33E6 sequences, 17 (17/450) nucleotide mutations were observed, 7 of which were synonymous mutations and 10 were nonsynonymous. C14T/G (T5I/S) was a triallelic mutation. Finally, in the 136 HPV33E7 sequences, 9 (9/294) nucleotide mutations were observed, 3 of which were synonymous mutations and 6 were nonsynonymous. C134T/A (A45V/E) and C278G/A (T93S/N) were triallelic mutations. Lineage A was the most common lineage in both HPV31 and HPV33. In all of the sequences, we only identified one positively selected site, HPV33 E6 (K93N). Most nonsynonymous mutations were localized at sites belonging to MHC and/or B-cell predicted epitopes. Data obtained in this study should contribute to the development and application of detection probes, targeted drugs, and vaccines.

Characterization of a Highly Virulent Noncytopathic Bovine Viral Diarrhea Virus 2b Isolate Detected in Cattle in Inner Mongolia, China

Bovine viral diarrhea virus (BVDV) infection causes subclinical to severe acute disease in cattle all over the world. Two genotypes of BVDV are recognized, BVDV1 and BVDV2. Currently, the subtypes of BVDV1b and BVDV2a are mainly circulating in China. Here, a newly noncytopathic (ncp) BVDV strain named BVDVNM21 was isolated and identified from cattle. We determined the complete genome sequence of BVDVNM21, phylogenetic analysis of 5′ untranslated region (5′UTR), Npro, and E2 gene, and complete genome showed the virus belongs to BVDV2b subtype and formed an independent clade within BVDV2b. Genome-wide sequence analysis showed that BVDVNM21 had high homology with SD1301 (98.10%) isolated from China. In the experimental infection study of guinea pigs and calves, they all developed similar clinical signs, including a pronounced and prolonged febrile response lasting more than 3 days and pronounced reduction in white blood cells (WBC) and platelets of more than 40%. Moreover, guinea pigs showed more acute infection characteristics after infection, and WBC decreased by more than 50% at 1 day postinfection (dpi), and they recovered in less than 3 days. The results indicated that the BVDVNM21 strain showed high virulence in calves. It was the first confirmed isolation of a highly pathogenic ncpBVDV2b in cattle, as well as the establishment of the BVDV-guinea pig model. This study may provide a basis for further research and control of the prevalence of BVDV2b in China.

The rPRRSV-E2 strain exhibited a low level of potential risk for virulence reversion.

Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) and Classical Swine Fever Virus (CSFV) are two important pathogens, which cause serious impact on swine industry worldwide. In our previous research, rPRRSV-E2, the recombinant PRRSV expressing CSFV E2 protein, could provide sufficient protection against the lethal challenge of highly pathogenic PRRSV and CSFV, and could maintained genetically stable in vitro. Here, to evaluate the virulence reversion potential risk, rPRRSV-E2 had been continuously passaged in vivo, the stability of E2 expression and virulence of the passage viruses were analyzed. The results showed that no clinical symptoms or pathological changes could be found in the inoculated groups, and there were no significant differences of viraemia among the test groups. Sequencing and IFA analysis showed that the coding gene of exogenous CSFV E2 protein existed in the passaged viruses without any sequence mutations, deletions or insertions, and could expressed steadily. It could be concluded that the foreign CSFV E2 gene in the genome of rPRRSV-E2 could be maintained genetically stable in vivo, and rPRRSV-E2 strain had relatively low level of potential risk for virulence reversion.

Development of TaqMan-based real-time PCR assay based on the E1 genefor the quantitative detection of the Getah virus.

To develop a sensitive, specific, and rapid approach for the detection Getah virus (GETV), a set of primers targeting the conserved region of the E1 gene was created. The TaqMan-based real-time PCR method for GETV detection was developed by optimizing the reaction conditions. The method demonstrated excellent specificity, and amplification did not occur with the causative agents of all prevalent swine viral infections (CSFV, PRRSV, PRV, PEDV, PTV, and JEV), except GETV. Additionally, upon assessing the sensitivity of the method, the minimum detection limit for GETV was found to be 5.94 copies/μL, which is 10 times higher than that of the traditional PCR approach. Further, the intra- and inter-assay variation coefficients were less than 1%, demonstrating good repeatability. Moreover, GETV was found in 10 of the 20 field serum samples using real-time PCR but only in three of the samples using traditional PCR. Consequently, the first GETV TaqMan-based real-time PCR approach based on the E1 gene was developed for GETV pathogenic diagnoses, and this exhibited high specificity, sensitivity, and repeatability. This assay is practical for the pathogenic diagnosis and epidemiology of GETV.

Abstract OT3-23-01: VELA: A first-in-human phase 1/2 study of BLU-222, a potent, selective cyclin-dependent kinase (CDK) 2 inhibitor in patients with cyclin E1 gene (CCNE1)-amplified or CDK4/6 inhibitor-resistant advanced solid tumors

Abstract Background The regulation of cell growth and proliferation is dependent on cyclins and CDKs. The formation of the cyclin D-CDK4/6 complex increases the expression of cyclin E1 and E2. Cyclin E1 and E2 bind to and activate CDK2; this results in a cyclin E/CDK2 complex that assists with downstream expression of DNA synthesis machinery. The use of CDK4/6 inhibitors such as palbociclib or ribociclib is an effective treatment in patients with hormone receptor-positive (HR+), human epithelial growth factor receptor-2 negative (HER2-) breast cancer; however, resistance to treatment eventually occurs. Aberrant cyclin E/CDK2 activity has been identified as a potential resistance mechanism by which tumors can evade CDK4/6 inhibitors. BLU-222 is an oral, investigational, potent, and selective CDK2 inhibitor. In preclinical studies, BLU-222 treatment in combination with ribociclib led to durable tumor regression in both CDK4/6-resistant and sensitive models of HR+HER2- breast cancer. Trial design VELA (NCT05252416) is an international, open-label, first-in-human phase 1/2 study evaluating the safety, tolerability, pharmacokinetics, pharmacodynamics, and efficacy of BLU-222 in adult patients with CCNE1-amplified tumors or with HR+HER2- breast cancer with disease progression on CDK4/6 inhibitors. In phase 1 and 2, patients aged ≥18 years with an Eastern Cooperative Oncology Group performance status 0–2 are eligible. In phase 2, all patients must have ≥1 measurable target lesion per Response Evaluation Criteria in Solid Tumors version 1.1. Primary endpoints include assessing the safety of BLU-222 as a single agent or BLU-222 in combination with either carboplatin or ribociclib and/or fulvestrant (phase 1 and 2), identifying the maximum tolerated dose and/or recommended phase 2 dose (phase 1), and determining the objective response rate (phase 2). In the phase 1 dose-escalation part, patients with any advanced solid tumor with progression on standard of care (SOC) will receive BLU-222; patients with gastric or endometrial cancer (EC) with progression on ≥2 prior therapies (including ≥1 platinum-based therapy) or with CCNE1-amplified platinum-resistant/refractory ovarian cancer (OC) will receive BLU-222 and carboplatin; patients with HR+HER- breast cancer with progression on CDK4/6 inhibitors will receive BLU-222, ribociclib, and fulvestrant. In the phase 2 dose-expansion part, patients with CCNE1-amplified tumors including EC (progression on ≥2 prior therapies), platinum-resistant/refractory OC, or other advanced solid tumors (progression after SOC) will receive BLU-222 monotherapy; patients with CCNE1-amplified platinum-resistant/refractory OC will receive BLU-222 and carboplatin; and patients with CDK4/6 inhibitor-resistant HR+HER2- breast cancer will receive BLU-222 and fulvestrant with/without ribociclib. Pharmacokinetic parameters will be calculated using standard non-compartmental methods from the plasma concentration–time data. Tissue biopsies will be collected during cycle 1 to assess the phosphorylation of retinoblastoma 1 (Rb1) protein which will be used as a pharmacodynamic marker to assess target inhibition. Dose escalation is ongoing and approximately 50 sites are anticipated to enroll patients across North America, Europe, and the Asia/Pacific region. Citation Format: Manish R Patel, Dejan Juric, Brian S Henick, Kathleen N Moore, Doreen Do, Joshua Chapman, Hui Zhang, Maria Roche, Kate J Newberry, Mikael Rinne, Timothy A Yap. VELA: A first-in-human phase 1/2 study of BLU-222, a potent, selective cyclin-dependent kinase (CDK) 2 inhibitor in patients with cyclin E1 gene (CCNE1)-amplified or CDK4/6 inhibitor-resistant advanced solid tumors [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr OT3-23-01.

Association Between E6 and E7 Human Papilloma Virus Type 16 Oncogen Mutations and P21 Protein Expression in Cervical Cancer

Cervical cancer is a disease characterized by the growth of abnormal cells in the cervical tissue. Cervical cancer is mostly caused by Human Papillomavirus (HPV) types 16 and 18. The role of genetic factors in the development of cervical malignancy is mediated by the presence of a mutation in the HPV 16 oncogene, especially oncogenes E6 and E7. Oncogenic proteins E6 and E7 in HPV initiate dysregulation of cellular proliferation and apoptotic mechanisms by targeting tumor suppressor proteins, such as the p21 protein. The purpose of this study was to assess the association between mutations in the E6 and E7 oncogenes of HPV-HR Type 16 and the pattern of p21 protein expression. This cross-sectional study was conducted at the Obstetrics and Gynecology Polyclinic of Prof. Dr. I.G.N.G. Ngoerah Hospital, from September 2020 to September 2021. The material taken was cervical cancer tissue from cervical cancer patients and then put into a preservative solution and then put in a cooler. DNA isolation was performed, and PCR was performed to determine positive and negative HPV. The amplification of the E6 and E7 genes was carried out before the sequencing and analysis of the E6 and E7 gene mutations was carried out. Then, immunohistochemical staining of p21 was carried out, followed by data analysis using SPSS for windows version 22.0. There were no significant differences in characteristics between the two groups. There was no association between mutations in the E6 and E7 HPV Type 16 oncogenes with p21 protein expression in cervical cancer cases (p-value 0.22).

Adult-Onset Renal Cell Carcinoma Associated with Xp11.2 Translocation/TFE3 Gene Fusion: 2 Case Reports and Review of Literature

Renal cell carcinoma (RCC) is the most common type of kidney cancer in adults, it represents 90-95% of neoplasms arising from the kidney. The Xp11.2 RCC translocation is a subtype of RCC that is defined by different translocations involving the Xp11.2 chromosome, all of which result in transcription factor E3 (TFE3) gene fusions. We presented 2 adult cases of Xp11-RCC, one patient had lymph node metastases and the second patient also had liver metastases. Both patients improved with surgical treatment by radical total nephrectomy with lymph node dissection, in addition to neoadjuvant medical treatment.

Deregulation of host gene expression by HPV16 E8^E2 knock-out genomes is due to increased productive replication

Productive replication of human papillomaviruses (HPV) only takes place in differentiating keratinocytes. The HPV16 E8^E2 protein acts as a repressor of viral gene expression and genome replication and HPV16 E8^E2 knock-out (E8-) genomes display enhanced viral late protein expression in differentiated cells. Global transcriptome analysis of differentiated HPV16 wild-type and E8-cell lines revealed a small number of differentially expressed genes which are not related to cell cycle, DNA metabolism or keratinocyte differentiation. The analysis of selected genes suggested that deregulation requires cell differentiation and positively correlated with the expression of viral late, not early transcripts. Consistent with this, the additional knock-out of the viral E4 and E5 genes, which are known to enhance productive replication, attenuated the deregulation of these host cell genes. In summary, these data reveal that productive HPV16 replication modulates host cell transcription.

The evolution of chikungunya virus circulating in Indonesia: Sequence analysis of the orf2 gene encoding the viral structural proteins.

Chikungunya virus (CHIKV) is an arthropod-borne virus that has caused several major epidemics globally, including in Indonesia. Although significant progress has been achieved in understanding the epidemiology and genotype circulation of CHIKV in Indonesia, the evolution of Indonesian CHIKV isolates is poorly understood. Thus, our study aimed to perform phylogenetic and mutation analyses of the orf2 gene encoding its viral structural protein to improve our understanding of CHIKV evolution in Indonesia. Complete orf2 gene sequences encoding the viral structural proteins of Indonesian-derived CHIKV were downloaded from GenBank until August 31, 2022. Various bioinformatics tools were employed to perform phylogenetic and mutation analyses of the orf2 gene. We identified 76 complete sequences of orf2 gene of CHIKV isolates originally derived from Indonesia. Maximum likelihood trees demonstrated that the majority (69/76, 90.8%) of Indonesian-derived CHIKV isolates belonged to the Asian genotype, while seven isolates (9.2%) belonged to the East/Central/South African (ECSA)genotype. The Indonesian-derived CHIKV isolates were calculated to be originated in Indonesia around 95 years ago (1927), with 95% highest posterior density (HPD) ranging from 1910 to 1942 and a nucleotide substitution rate of 5.07 × 10-4 (95% HPD: 3.59 × 10-4 to 6.67 × 10-4). Various synonymous and non-synonymous substitutions were identified in the C, E3, E2, 6K, and E1 genes. Most importantly, the E1-A226V mutation, which has been reported to increase viral adaptation in Aedes albopictus mosquitoes, was present in all ECSA isolates. To our knowledge, our study is the first comprehensive research analyzing the mutation and evolution of Indonesian-derived CHIKV based on complete sequences of the orf2 genes encoding its viral structural proteins. Our results clearly showed a dynamic evolution of CHIKV circulating in Indonesia.

An in vitro carcinogenesis model for cervical cancer harboring episomal form of HPV16.

Deregulated expression of viral E6 and E7 genes often caused by viral genome integration of high-risk human papillomaviruses (HR-HPVs) into host DNA and additional host genetic alterations are thought to be required for the development of cervical cancer. However, approximately 15% of invasive cervical cancer specimens contain only episomal HPV genomes. In this study, we investigated the tumorigenic potential of human cervical keratinocytes harboring only the episomal form of HPV16 (HCK1T/16epi). We found that the HPV16 episomal form is sufficient for promoting cell proliferation and colony formation of parental HCK1T cells. Ectopic expression of host oncogenes, MYC and PIK3CAE545K, enhanced clonogenic growth of both early- and late-passage HCK1T/16epi cells, but conferred tumor-initiating ability only to late-passage HCK1T/16epi cells. Interestingly, the expression levels of E6 and E7 were rather lower in late-passage than in early-passage cells. Moreover, additional introduction of a constitutively active MEK1 (MEK1DD) and/or KRASG12V into HCK1T/16epi cells resulted in generation of highly potent tumor-initiating cells. Thus an in vitro model for progression of cervical neoplasia with episomal HPV16 was established. In the model, constitutively active mutation of PIK3CA, PIK3CAE545K, and overexpression of MYC, in the cells with episomal HPV16 genome were not sufficient, but an additional event such as activation of the RAS-MEK pathway was required for progression to tumorigenicity.

Characteristics of human papillomavirus infection among females and the genetic variations of HPV18 and HPV58 in Henan province, China

The present study aims to investigate the genotype distribution of Human papillomavirus (HPV) and variations of HPV18 and HPV58 infection among 6538 females in Luoyang city during 2019–2021. The overall positive rate of females with HPV infection was 12.34%, with 9.74% were infected with single HPV and 2.60% with multiple HPVs. The prevalent rate of high-risk HPV (HR-HPV) was 9.85% and the top five HR-HPV genotypes were HPV52 (1.94%), HPV16 (1.93%), HPV58 (1.48%), HPV51 (1.02%) and HPVV39 (0.99%). Two peaks of HPV infections rates were observed in females aged ≤ 20 and 61–65 years old. To characterize mutations, 39 HPV18 and 56 HPV58 L1, E6 and E7 genes were sequenced and submitted to GenBank. In the HPV18 E6-E7-L1 sequences, 38 nucleotides changes were observed with 10/38 were non-synonymous mutations (5 in E6 gene, 1 in E7 gene and 4 in L1 gene). In the HPV58 E6-E7-L1 sequences, 53 nucleotides changes were observed with 23/53 were non-synonymous mutations (3 in E6 gene, 5 in E7 gene and 15 in L1 gene). Phylogenetic analysis based on L1 gene showed that 92.3% (36/39) of HPV18 isolates fell into sublineage A1 and 7.7% (3/39) belonged to A5. For HPV58, 75.0% (42/56) isolates belonged to sublineage A1 and 25.0% (14/56) were sublineage A2. There was no association between amino mutation and cervical lesions. The present study provides basic information about the distribution, genotypes and variations of HPV among females population in Luoyang city, which would assist in the formulation of HPV screening and vaccination programs and preventive strategies for HPV-attributable cancer in this region.

Genetic variation in four maturity genes and photoperiod insensitivity effects on the yield components and on the growth duration periods of soybean

Soybean (Glycine max (L.) Merr.) is a typical short-day and thermophilic crop. Absence of or low sensitivity to photoperiod is necessary for short-day crops to adapt to high latitudes. Photoperiod insensitivity in soybeans is controlled by two genetic systems and involves three important maturity genes: E1, a repressor for two soybean orthologs of Arabidopsis FLOWERING LOCUS T, and E3 and E4, which are phytochrome A genes. The aim of this work was to investigate the role of four maturity genes (E1 through E4) on the yield components, seed quality and on phasic development of near isogenic by E genes lines of soybean: short-day (SD) lines with genotype e1E2E3E4e5E7, e1E2E3e4e5E7, E1e2e3E4e5E7 and photoperiodic insensitive (PPI) lines with genotype e1e2E3E4e5E7, e1e2e3E4e5E7 under a long photoperiod (the natural day length of 50 latitude) conditions and short day conditions. The results of the study showed that soybean development processes under conditions of different day lengths depend on the dominant/recessive state of the main maturity genes. In addition, the response to the photoperiod depends on certain combinations of genes. SD lines began flowering on average 16.9% later under the conditions of a natural long photoperiod. Dominant alleles of genes E1 and E3 extended the pre- and post-flowering phases under conditions of exposure to long and short photoperiods. The dominant allele of the E1 gene delayed the onset of flowering by an average of 26.9%, and the period of full maturity by 39.8% compared to the recessive e1. The dominant allele of the E3 gene, compared to the recessive e3, lengthened the transition to flowering by an average of 16.1%, and the period of full ripeness by 27.1%. The dominant allele of the E2 gene lengthened the duration of the vegetative phase by 20% under the conditions of a long photoperiod. No significant influence of the dominant E4 allele on the duration of the vegetative and generative phases of soybean development was found in our study. PPI lines begin flowering under the conditions of a long and short photoperiod at the same time, but the phases of flowering and full seed maturity in the line with genotype e1e2e3E4e5E7 occurred earlier, due to the loss of the photoperiod sensitivity of the E3 gene. PPI line with genotype e1e2e3E4e5E7 proved to be the most insensitive line to the effect of different photoperiod durations among the studied lines. It was shown that the dominant alleles of E1–E4 maturity genes reduced the parameters of seed weight per plant and the weight of 1000 seeds under the conditions of a natural long photoperiod in comparison with recessive alleles of these genes. The maximum weight of seeds per plant and the weight of 1000 seeds were recorded in the PPI line with genotype e1e2e3E4e5E7. It should be noted that the dominant alleles E1 and E3 increased yield under conditions of a short photoperiod. Maturity genes had different effects on the biochemical composition of seeds. It was shown that soybean lines with dominant E1, E2 and E4 genes showed a higher content of starch and a lower content of total nitrogen and oil in seeds under natural photoperiod conditions compared to lines with recessive alleles of these genes. The dominant E3 allele reduced the oil content and did not affect the starch and total nitrogen content of seeds under long day conditions compared to the recessive e3 allele. The analysis of the effect of photoperiod on the timing of phenophases, yield structure indicators and biochemical composition of seeds in soybean plants with different sensitivity to photoperiod showed that the PPI line with the genotype e1e2e3E4e5E7 was the most adapted to the natural conditions of 50 degrees latitude. The PPI line with the genotype e1e2e3E4e5E7 was characterized by the shortest phases of days from sowing to flowering and full maturity. As a result, this line had the shortest growing season without reducing the yield and seed quality. Clearly, photoperiod had strong effects on all stages of plant reproduction and often acted indirectly, as shown by delayed responses expressed in later phases of development. The obtained results can be useful for the selection of soybean cultivars adapted to the climatic conditions of cultivation of Kharkiv region.

A conventional PCR-based method to detect the E2 gene of the rubella virus for epidemiological analysis.

To eliminate the rubella virus (RV), genetic characterization is vital for its detection, identification of endemic transmission, and diagnosis of imported cases. The 739-nucleotide region in the E1 gene has primarily been used for genotyping for epidemiological analysis. However, in the 2018-2019 RV outbreak, identical sequences were observed in patients who were not epidemiologically linked. Additionally, the 739 nt sequences from the outbreak in Tokyo in 2018-2019 were identical to RV identified in China in 2019. This suggests that this region may be insufficient to identify the detected RV strains as endemic or imported. In 62.4% of the specimens, the E1 gene sequences of the 1E RV genotype were identical. Additionally, the observed discordance of sequences from the mainly detected identical sequence in the 739-nt sequence of the E1 gene were one (31.0%), two (3.5%), three (2.6%), and four (0.23%). Moreover, a comparison of the complete structural protein-coding region suggests that the E2 gene is more diverse than the E1 and the capsid gene. Thus, conventional polymerase chain reaction (PCR) primers were developed to detect the E2 gene and improve epidemiological analysis. A comparison of the sequences identified during the RV outbreak in Tokyo revealed genetic differences in the sequences (15 of the 18 specimens). These results suggest that additional information could be obtained by simultaneously analyzing the E2 and the E1 region. The identified sequences can potentially aid in evaluating the RV strains detected during epidemiological analysis.

Novel canonical and non-canonical viral antigens extend current targets for immunotherapy of HPV-driven cervical cancer

Current immunotherapeutic approaches for human papillomavirus (HPV)-driven cervical cancer target the viral oncogenes E6 and E7. We report viral canonical and alternative reading frame (ARF)-derived sequences presented on cervical tumor cells, including antigens encoded by the conserved viral gene E1. We confirm immunogenicity of the identified viral peptides in HPV-positive women, and women with cervical intraepithelial neoplasia. We observe consistent transcription of the E1, E6, and E7 genes in 10 primary cervical tumor resections from the four most common high-risk HPV subtypes (HPV16, 18, 31, and 45), suggesting the suitability of E1 as therapeutic target. We finally confirm HLA presentation of canonical peptides derived from E6 and E7, and ARF-derived viral peptides from a reverse-strand transcript spanning the HPV E1 and E2 genes in primary human cervical tumor tissue. Our results extend currently known viral immunotherapeutic targets in cervical cancer and highlight E1 as an important cervical cancer antigen.

Overview of genetic and epigenetic regulation of human papillomavirus and apoptosis in cervical cancer.

Cervical cancer is the fourth most common cancer affecting women worldwide after breast, colorectal and lung cancers. Owing to a lack of awareness and resources, low- and middle-income countries bear most of the burden of cervical cancer. In developed countries, the incidence rate has been halved over the past three decades due to robust screening and implementation of vaccine programs. HPV is not the sole cause of cervical cancer but acts as a principal factor in the pathogenesis of cervical cancer. By integrating into the host genome, its oncogenic proteins (E6 and E7) alter and interfere with the standard signal transduction machinery of the host. Apoptosis is a key pathway affected by aberrant genetic mutations, polymorphisms and epigenetic mechanisms during cervical carcinogenesis. Along with DNA methylation and histone modifications, non-coding RNAs have also been implicated as epigenetic modulators in various malignancies and are being explored for reversing disease severity. This review emphasizes various genetic and epigenetic approaches regulating apoptotic pathways and HPV E6 and E7 genes that can be targeted to overcome the challenges in cervical cancer treatment. In addition, it also discusses the apoptosis targeting novel drug molecules in cervical cancer which are currently undergoing clinical and pre-clinical trials.

Genotypic distribution of human papillomavirus and phylogenetic analysis of E6 and E7 gene of HR-HPV variants isolated from Pakistani population

High-risk-human papillomavirus (HR-HPV)-induced cervical cancer is the second most common cause of death among females worldwide. HPV16 is the most prevalent HR-HPV infection worldwide. This study found the genotypic distribution of HR-HPV in the local population and investigated the sequence variations among the E6 and E7 oncogenes of the local HPV16 genotype to the E6 and E7 oncogenes of the foreign HPV16 genotypes and constructed a phylogenetic relationship based on nucleotide sequence comparison among the variants identified in our study along with previously reported isolates that were obtained from different regions of the world. The samples were collected from patients with cervical cancer. Genomic DNA was extracted, and HR-HPV genotypes were determined using real-time PCR. The HPV16 E6 and E7 genes were amplified and sequenced. A HPV16 phylogenetic tree was constructed using the maximum likelihood method with MEGA 7. HPV16 was the most prevalent human papillomavirus (HPV) type identified in the present study. HPV16 isolates belonged to the A1 sublineage of the European branch. Twenty-one nucleotide sequences were included in this analysis. The first, second, and third codon positions are also included. The final dataset included 776 positions.