Genomic analysis of SARS-CoV-2 omicron sublineage BA.5.2.1 in Erbil/Iraq.

Due to several mutations in its genomic sequence, particularly in the spike protein region, the recently-discovered SARS-CoV-2 variant B.5.2.1 has alarmed health policy authorities worldwide. The World Health Organization (WHO) has labelled it "Omicron" and classified it as a worldwide variant of concern (VOC). Following the appearance of Omicron in Iraq, new cases were also detected and analyzed in Kurdistan regions. Two hundred patients were recruited in this study from Erbil/Iraq. The RNA genome samples were extracted,  the qRT-PCR performed, and 10 samples were sequenced. The sample sequence was published (EPI ISL 15921492) in the GISAID international gene bank for COVID-19. When compared to the BA.1 Omicron sublineage, 17 new mutations and five deletions in the  Omicron subvariant BA.5.2.1 sequence were detected. The spike region includes eight of these variations and one deletion. Overall, 30 substitutions were shared between those previously seen in the BA.1 sublineage and the newly-detected BA.5.2.1 Omicron subvariant. We detected eight new substitutions in our BA.5.2.1 subvariants (T112I, A27S, V213G, T376F, D405N, R408S, L452R, F486V), which were not mentioned previously, should be cause for concern and may be related to immune escape or viral oligomerization. Omicron might be more immune-escape-capable than the current VOCs/VOIs. However, the predicted mutational research shows no conclusive evidence that the Omicron variant may be more virulent or fatal than other variations, including Delta. The greater capacity for immunological evasion may cause the current increase in Omicron cases in Erbil/Iraq.

Comparison of Antibody Levels Produced by Pfizer, AstraZeneca, and Sinopharm Vaccination in COVID-19 Patients in Erbil City-Iraq.

In this study, early adverse impacts that emerged after vaccination with each dose of these vaccines were compared from previously infected participants. Ant-SARS-CoV-2 spike-specific IgG and IgA antibodies produced by these three vaccines have been assessed using ELISA method at different time periodsꓼ including pre-vaccination, 25 days after the first shot of vaccination and 30 days after the second shot of vaccination with Pfizer-BioNTech, AstraZeneca, and Sinopharm vaccine. Overall, 150 previously infected cases were studied, 50 cases received Pfizer vaccine, 50 cases received AstraZeneca vaccine, and 50 cases received Sinopharm vaccine. The findings showed that a higher number of vaccinated participants with AstraZeneca and Pfizer vaccine had tired/fatigue/lethargy, headache, fever, and sore in arm at the first shot, but milder adverse effects, such as headaches, fever, and sore in arm, were detected in the data on the Sinopharm vaccine's adverse impacts. At the second dose, a lower number of vaccinated cases with AstraZeneca and Pfizer vaccine reported higher frequencies of the side effects. However, the results showed that the level of anti-spike-specific IgG and IgA antibodies produced by vaccinated patients with Pfizer vaccine increased compared to those who vaccinated with AstraZeneca and Sinopharm vaccine from 25 days after the first dose. From 30 days after the second dose, the IgG and IgA antibodies were significantly boosted in 97% of vaccinated patients with Pfizer vaccine compared to 92% of those who vaccinated with AstraZeneca vaccines and 60% of those who vaccinated with Sinopharm. In conclusion, these results confirmed that two doses of the Pfizer, and AstraZeneca vaccine induce a higher response of IgG and IgA antibodies than that induced by Sinopharm vaccines.

The profiles of miR-4510 expression level in breast cancer.

MicroRNA that is abnormally produced in breast cells can disrupt biological processes, which can lead to cancer. This study aims to screen differentially expressed genes (DEGs) and ncRNAs (DEncRNAs) in the formalin-fixed paraffin-embedded (FFPE) tissues of breast cancer (BC) as compared with the normal adjacent tissues (NAT), and identify miR-4510 as a novel biomarker of BC. This study looked at differentially expressed genes (DEGs) using MACE-Seq and differentially expressed ncRNAs (DEncRNAs) using the small RNA-Seq. Real-time qPCR was used to determine the level of expression of miR-4510. In this study, MACE-Seq results showed that 26,795 genes, with a p-value < 0.05, were differentially expressed in BC paraffin tissues as compared with NAT. Small RNA-Seq results revealed that 1326 ncRNAs, with a p-value < 0.05, were differentially expressed. We confirmed that miR-4510 was significantly down-expressed (p-value = 0.001) by qRT-PCR in the paraffin tissue of 120 BC patients. Based on eleven computational prediction programs, TP53, TP53INP1, MMP11, and COL1A1 for the miR-4510 were identified as miR-4510 targets. The MACE-seq result showed that the gene of TP53 (p-value = 0.001) and TP53INP1 (p-value = 0.02) was significantly down-regulated, but the gene of MMP11 (p-value = 0.004) and COL1A1 (p-value = 0.0001) was significantly over-expressed in 20 paired specimens of the BC and NAT. We discovered that a single SNP inside the miR-4510 binding site occurred only in BC, in which Guanine (G) changed into Adenine (A). Two SNPs outside the miR-4510 binding site occurred, and Guanine (G) in both BC and NAT was changed into Thymine (T), as compared to the reference sequence (RefSeq). Overall, our results suggested that miR-4510 functions as a tumor suppressor in the BC. Mir-4510 may act as a tumor suppressor, however additional experimental data is needed to corroborate these assumptions and can be exploited as a biomarker for BC.

SARS-CoV-2 Omicron Variant Genomic and Phylogenetic Analysis in Iraqi Kurdistan Region.

Omicron variants have been classified as Variants of Concern (VOC) by the World Health Organization (WHO) ever since they first emerged as a result of a significant mutation in this variant, which showed to have an impact on transmissibility and virulence of the virus, as evidenced by the ongoing modifications in the SARS-CoV-2 virus. As a global pandemic, the Omicron variant also spread among the Kurdish population. This study aimed to analyze different strains from different cities of the Kurdistan region of Iraq to show the risk of infection and the impact of the various mutations on immune responses and vaccination. A total of 175 nasopharyngeal/oropharyngeal specimens were collected at West Erbil Emergency Hospital and confirmed for SARS-CoV-2 infection by RT-PCR. The genomes of the samples were sequenced using the Illumina COVID-Seq Method. The genome analysis was established based on previously published data in the GISAID database and compared to previously detected mutations in the Omicron variants, and that they belong to the BA.1 lineage and include most variations determined in other studies related to transmissibility, high infectivity and immune escape. Most of the mutations were found in the RBD (receptor binding domain), the region related to the escape from humoral immunity. Remarkably, these point mutations (G339D, S371L, S373P, S375F, T547K, D614G, H655Y, N679K and N969K) were also determined in this study, which were unique, and their impact should be addressed more. Overall, the Omicron variants were more contagious than other variants. However, the mortality rate was low, and most infectious cases were asymptomatic. The next step should address the potential of Omicron variants to develop the next-generation COVID-19 vaccine.

RNA Sequencing-Based Total RNA Profiling; The Oncogenic MiR-191 Identification as a Novel Biomarker for Breast Cancer.

This study aims to screen the differential expression of total RNA transcripts in formalin-fixed paraffin-embedded tissues (FFPETs) in breast cancer (BRCA) and normal adjacent tissues (NATs) and identify miR-191 as a new biomarker for early diagnosing BRCA. Differentially expressed genes (DEGs) by MACE-Seq and differentially expressed ncRNAs (DEncRNAs) by the TrueQuant technique were examined in this study. The miR-191 expression level was measured by Real Time-qPCR. An average of 4,739 coding genes from 25,713 significantly down-regulated genes was identified, whereas 3,954 coding genes were significantly up-regulated in the BRCA against NAT. An average of 1450 ncRNAs, including up-regulated= 679 and down-regulated= 780, were differentially expressed in 7 paired samples of BRCA and NAT. Among the ncRNAs, 227 microRNAs, including unchanged= 152, down=53, and up=22, were differentially expressed. MiR-191 was one of the 22 significant up-regulation, with p=0.0001. RT-qPCR results confirmed that miR-191, p=0.003, was significantly over-expressed in 120 paired samples of BRCA and NAT. Furthermore, NextSeq 500 revealed that a single nucleotide polymorphism (C>T) newly occurred in the mature sequence of miR-191-5p seed region in BRCA samples. However, the putative target genes regulated by the miR-191-5p were recognized by the above ten computational programs for the prediction. MACE-Seq outcomes showed that the genes of CDK6(P=0.0001), DAPK1(P=0.02), MTC7(P=0.04), SETD1B(P=0.005), CALN1(P=0.01), and TMOD2(P=0.001) were significantly over-expressed in the BRCA against the NATs. The expression level of the targets was adversely related to the miR-191-5p.

MACE-Seq-based coding RNA and TrueQuant-based small RNA profile in breast cancer: tumor-suppressive miRNA-1275 identified as a novel marker.

INTRODUCTION: Disruption of cellular processes in the breast by abnormally expressed miRNA is characterized to develop cancer. We aimed to identify the differential expression of small RNAs (sRNAs) and mRNAs in formalin-fixed paraffin-embedded (FFPE) tissue of the breast cancer (BC) and normal adjacent tissue (NAT). Another aim is to determine the differential expression of miR-1275 as a novel biomarker for BC and also identify its target genes. METHODS: TrueQuant method for analysis of sRNA expression and MACE-sequencing method for analysis of gene expression were used analyzing. The RT-qPCR technique was used to confirm miR-1275 down expression. Target genes of miR-1275 were computationally identified using target prediction sites and also the expression level of them was experimentally determined among the expressed genes. RESULTS: TrueQuant findings showed that 1400 sRNAs were differentially expressed in the FFPE tissue of two Kurdish cases with BC, as compared to NAT. Among the sRNAs, 29 small RNAs were shown to be significantly downregulated in BC cells. The RT-qPCR results confirmed that miR-1275 was significantly down-expressed in 20 Kurdish cases with BC compared to NAT. However, Overall survival (OS) analysis revealed that the correlation between the expression level of miR-1275 and clinical significance was highly corrected in cases with BC (OS rate: P = 0.0401). The MACE-seq results revealed that 26,843 genes were differentially expressed in the BC tissue compared to NAT, but 7041 genes were displayed in a scatter plot. Furthermore, putative target genes (DVL3, PPP2R2D, THSD4, CREB1, SYT7, and PRKACA) were computationally identified as direct targets of miR-1275 in several target predicted sites. The MACE-seq results revealed that the expression level of these targets was increased in BC tissue compared to NAT. The level of these targets was negatively associated with miR-1275 expression. Finally, the role of down-regulated miR-1275 on its targets in biological mechanisms of BC cells was identified; including cell growth, proliferation, movement, invasion, metastasis, and apoptosis. CONCLUSION: Down-expressed miR-1275, a tumor suppressor, is a novel biomarker for early detection of BC. DVL3, PPP2R2D, THSD4, CREB1, SYT7, and PRKACA are newly identified to be targeted by miR-1275.