Characterization of a base-resolution common deletion region within CDKN2A gene in cancers and its biological and clinical significances

Background: Frequency of somatic copy number deletion of CDKN2A gene is upto 60% in human esophageal squamous cell cancer. However, it is unknown whether CDKN2A deletion could be a biomarker for esophageal squamous cell dysplasia (ESCdys) due to absence of a feasible detection method. Methods: Information on base-resolution common deletion region (CDR) for CDKN2A were extracted from published articles and confirmed with whole genome sequencing (WGS). A quantitative PCR targeted to the CDR (P16-Light) was established and used to detect CDKN2A copy number in ESCdys biopsies from patients (n=205) enrolled in a multicentre follow-up study. Results: A 5.1-kb CDR from the CDKN2A/P16INK4A promoter to intron-2 was firstly characterized in 90% (83/92) of cancer cell lines and confirmed with WGS. The CDR covers CDKN2A exon-2 which is the essential coding exon for both P16INK4a and P14ARF. And CDKN2A exon-2 deletion markedly promoted the proliferation and invasion and inhibited the apoptosis of HEK293T cells. In the follow-up study, both somatic CDKN2A deletion and amplification are prevalent in mild/moderate (m/M) ESCdys. CDKN2A deletion was less common among 70 patients whose ESCdys regressed than among 135 patients whose ESCdys progressed or remained stable, and CDKN2A amplification was more common in the patients who regressed than in the patients whose m/M ESCdys persisted or progressed over a median of 37 months of follow-up (p<0.0001). Conclusion: There is A 5.1-kb CDR within CDKN2A gene in many cancers. CDR deletion could inactivate both P16INK4a and P14ARF and associate with prognosis of ESCdys.

Spread of Endemic SARS-CoV-2 Lineages in Russia Before April 2021

In 2021, the COVID-19 pandemic is characterized by global spread of several lineages with evidence for increased transmissibility. Russia is among the countries with the highest number of confirmed COVID-19 cases, making it a potential hotspot for emergence of novel variants. Here, we show that among the globally significant variants of concern, alpha (B.1.1.7), beta (B.1.351) or gamma (P.1), none have been sampled in Russia before January 2021. Instead, between summer 2020 and spring 2021, the epidemic in Russia has been characterized by the spread of two lineages that are rare elsewhere: B.1.1.317 and a sublineage of B.1.1 including B.1.1.397 (hereafter, B.1.1.397+). Their frequency has increased in different parts of Russia. Mutational composition and frequency dynamics suggest that B.1.1.317 and B.1.1.397+ may be more transmissible than the previously predominant B.1.1. On top of these lineages, in January 2021, B.1.1.7 emerged in Russia, reaching the frequency of 17.4% (95% C.I.: 12.0%-24.4%) in March 2021. Additionally, we identify three novel distinct lineages, AT.1, B.1.1.524 and B.1.1.525, that have started to spread, together reaching the frequency of 11.8% (95% C.I.: 7.5%-18.1%) in March 2021. These lineages carry combinations of several notable mutations, including the S:E484K mutation of concern, deletions at a recurrent deletion region of the spike glycoprotein (S:Δ140-142, S:Δ144 or S:Δ136-144), and nsp6:Δ106-108 (also known as ORF1a:Δ3675-3677). Community-based PCR testing indicates that these variants have continued to spread in April 2021, with the frequency of B.1.1.7 reaching 21.7% (95% C.I.: 12.3%-35.6%), and the joint frequency of B.1.1.524 and B.1.1.525, 15.2% (95% C.I.: 7.6%-28.2%). Although these variants have been displaced by the onset of delta variant in May-June 2021, the frequency increase of lineages B.1.1.317, B.1.1.397+, AT.1, B.1.1.524 and B.1.1.525 suggest that the combinations of mutations observed in them could have increased the rate of their spread.

Spread of endemic SARS-CoV-2 lineages in Russia

In 2021, the COVID-19 pandemic is characterized by global spread of several lineages with evidence for increased transmissibility. Russia is among the countries with the highest number of confirmed COVID-19 cases, making it a potential hotspot for emergence of novel variants. Here, we show that among the globally significant variants of concern, B.1.1.7 (501Y.V1), B.1.351 (501Y.V2) or P.1 (501Y.V3), none have been sampled in Russia before January 2021. Instead, since summer 2020, the epidemic in Russia has been characterized by the spread of two lineages that are rare elsewhere: B.1.1.317 and a sublineage of B.1.1 including B.1.1.397 (hereafter, B.1.1.397+). In February-March 2021, these lineages reached frequencies of 26.9% (95% C.I.: 23.1%-31.1%) and 32.8% (95% C.I.28.6%-37.2%) respectively in Russia. Their frequency has increased in different parts of Russia. Together with the fact that these lineages carry several spike mutations of interest, this suggests that B.1.1.317 and B.1.1.397+ may be more transmissible than the previously predominant B.1.1, although there is no direct data on change in transmissibility. Comparison of frequency dynamics of lineages carrying subsets of characteristic mutations of B.1.1.317 and B.1.1.397+ suggests that, if indeed some of these mutations affect transmissibility, the transmission advantage of B.1.1.317 may be conferred by the (S:D138Y+S:S477N+S:A845S) combination; while the advantage of B.1.1.397+ may be conferred by the S:M153T change. On top of these lineages, in January 2021, B.1.1.7 emerged in Russia, reaching the frequency of 17.4% (95% C.I.: 12.0%-24.4%) in March 2021. Additionally, we identify three novel distinct lineages, AT.1, and two lineages prospectively named B.1.1.v1 and B.1.1.v2, that have started to spread, together reaching the frequency of 11.8% (95% C.I.: 7.5%-18.1%) in March 2021. These lineages carry combinations of several notable mutations, including the S:E484K mutation of concern, deletions at a recurrent deletion region of the spike glycoprotein (S:Δ140-142, S:Δ144 or S:Δ136-144), and nsp6:Δ106-108 (also known as ORF1a:Δ3675-3677). Community-based PCR testing indicates that these variants have continued to spread in April 2021, with the frequency of B.1.1.7 reaching 21.7% (95% C.I.: 12.3%-35.6%), and the joint frequency of B.1.1.v1 and B.1.1.v2, 15.2% (95% C.I.: 7.6%-28.2%). The combinations of mutations observed in B.1.1.317, B.1.1.397+, AT.1, B.1.1.v1 and B.1.1.v2 together with frequency increase of these lineages make them candidate variants of interest.

Whole-exome sequencing reveals potential germline and somatic mutations in 60 malignant ovarian germ cell tumors

Background Malignant ovarian germ cell tumors (MOGCTs) are rare and heterogeneous ovary tumors. We aimed to identify potential germline mutations and somatic mutations in MOGCTs by whole-exome sequencing. Methods The peripheral blood and tumor samples from these patients were used to identify germline mutations and somatic mutations, respectively. For those genes corresponding to copy number alterations (CNA) deletion and duplication region, functional annotation of was performed. Immunohistochemistry was performed to evaluate the expression of mutated genes corresponding to CNA deletion region. Results In peripheral blood, copy number loss and gain were mostly found in yolk sac tumors (YST). Moreover, POU5F1 was the most significant mutated gene with mutation frequency &gt; 10% in both CNA deletion and duplication region. In addition, strong cytoplasm staining of POU5F1 (corresponding to CNA deletion region) was found in 2 YST and nuclear staining in 2 dysgerminomas (DG) tumor samples. Genes corresponding to CNA deletion region were significantly enriched in the signaling pathway of regulating pluripotency of stem cells. In addition, genes corresponding to CNA duplication region were significantly enriched in the signaling pathways of RIG-I-like receptor, Toll-like receptor, NF-kappa B and Jak–STAT. KRT4, RPL14, PCSK6, PABPC3 and SARM1 mutations were detected in both peripheral blood and tumor samples. Conclusions Identification of potential germline mutations and somatic mutations in MOGCTs may provide a new field in understanding the genetic feature of the rare biological tumor type in the ovary.