Molecular transition of SARS-CoV-2 from critical patients during the first year of the COVID-19 pandemic in Mexico City

Background

The SARS-CoV-2 virus has caused unprecedented mortality since its emergence in late 2019. The continuous evolution of the viral genome through the concerted action of mutational forces has produced distinct variants that became dominant, challenging human immunity and vaccine development.

Aim and methods

In this work, through an integrative genomic approach, we describe the molecular transition of SARS-CoV-2 by analyzing the viral whole genome sequences from 50 critical COVID-19 patients recruited during the first year of the pandemic in Mexico City.

Results

Our results revealed differential levels of the evolutionary forces across the genome and specific mutational processes that have shaped the first two epidemiological waves of the pandemic in Mexico. Through phylogenetic analyses, we observed a genomic transition in the circulating SARS-CoV-2 genomes from several lineages prevalent in the first wave to a dominance of the B.1.1.519 variant (defined by T478K, P681H, and T732A mutations in the spike protein) in the second wave.

Conclusion

This work contributes to a better understanding of the evolutionary dynamics and selective pressures that act at the genomic level, the prediction of more accurate variants of clinical significance, and a better comprehension of the molecular mechanisms driving the evolution of SARS-CoV-2 to improve vaccine and drug development.

Abstract 6003: Study of secondary epimutations in cis of the promoter in germline tumor suppressor genes as a cause of hereditary breast and ovarian cancer

Cancer is a multifactorial and highly heterogeneous disease. Breast cancer (BC) is the main malignant neoplasm in women and has the highest incidence and mortality rates worldwide. About 10% of all BC cases are hereditary and its most common form is Hereditary Breast and Ovarian Cancer Syndrome (HBOC).In a study conducted by our research group in a cohort of 300 Mexican women with HBOC using a panel of 143 genes of susceptibility to different types of cancer (Quezada-Urban et al., 2018), we found that 74% of patients were negative for variants in the coding regions and only 15% of patients had at least one pathogenic variant in 18 different genes. In several types of hereditary cancer syndromes, it has been shown that germline genetic alterations such as single nucleotide variations, and indels in cis of the promoter region of tumor suppressor genes modify the methylation pattern and cause epigenetic silencing and the concomitant somatic loss of heterozygosity. These events are known as secondary cis epimutations and represent an alternative mechanism of molecular pathogenesis in patients with hereditary cancer syndromes. In this work we are investigating in germline gDNA the methylation profile in the promoter region of 18 tumor suppressor genes in 231 patients negative for pathogenic variants and 156 matched controls by using direct bisulfite massive parallel sequencing. So far, we have extracted gDNA and treated with sodium bisulfite from all patient and control samples. From the converted gDNA, we amplified the promoter region of the 18 study genes by PCR (9,675 endpoint PCR products). We have prepared a total of 387 genomic libraries from which we perform massive sequencing and bioinformatic analysis of 229 patients, 74 controls and 2 positive controls. Currently, we have found 4 patients with promoter hypermethylation in the RAD51C, POLH, EPCAM, and BRCA1 genes that can be generated by a secondary cis epimutation. We have found statistically significant differences in the methylation levels of the promoter regions of the BRCA1/2, PMS2, FANCI, MLH1, PALB2, POLH, ERCC3, ATM, MSH2, BRIP1, and EPCAM genes in patients compared with controls. This result suggests that low level basal methylation marks could be potential biomarkers of HBOC pathogenesis. Interestingly, our studies indicate that hypermethylation at the promoter of MSH2, PALB2, BRIP1, and EPCAM are associated with HBOC risk, and that specific hypermethylation at the CpG sites of MSH2 and PALB2 (cg47630224 and cg23652916, respectively), could be potential biomarkers in HBOC risk. Lastly, according to preliminary in silico results, the co-occurrence of site-specific hypermethylation in MSH2 and PALB2 is possibly due to the absence of interaction of the common transcription factor SP4 in a GC-box site. These findings expand our vision of the genetic and epigenetic mechanisms of susceptibility to this disease.

Citation Format: Miguel Ruiz De La Cruz, Héctor Martínez Gregorio, Clara Estela Díaz Velásquez, Aldo Hugo De La Cruz Montoya, Fidel de la Cruz Hernández-Hernández, Felipe Vaca Paniagua. Study of secondary epimutations in cis of the promoter in germline tumor suppressor genes as a cause of hereditary breast and ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6003.

Cis-Acting Factors Causing Secondary Epimutations: Impact on the Risk for Cancer and Other Diseases

Epigenetics affects gene expression and contributes to disease development by alterations known as epimutations. Hypermethylation that results in transcriptional silencing of tumor suppressor genes has been described in patients with hereditary cancers and without pathogenic variants in the coding region of cancer susceptibility genes. Although somatic promoter hypermethylation of these genes can occur in later stages of the carcinogenic process, constitutional methylation can be a crucial event during the first steps of tumorigenesis, accelerating tumor development. Primary epimutations originate independently of changes in the DNA sequence, while secondary epimutations are a consequence of a mutation in a cis or trans-acting factor. Secondary epimutations have a genetic basis in cis of the promoter regions of genes involved in familial cancers. This highlights epimutations as a novel carcinogenic mechanism whose contribution to human diseases is underestimated by the scarcity of the variants described. In this review, we provide an overview of secondary epimutations and present evidence of their impact on cancer. We propose the necessity for genetic screening of loci associated with secondary epimutations in familial cancer as part of prevention programs to improve molecular diagnosis, secondary prevention, and reduce the mortality of these diseases.

Latin American Study of Hereditary Breast and Ovarian Cancer LACAM: A Genomic Epidemiology Approach

Purpose: Hereditary Breast and Ovarian Cancer (HBOC) syndrome is responsible for ~5-10% of all diagnosed breast and ovarian cancers. Breast cancer is the most common malignancy and the leading cause of cancer-related mortality among women in Latin America (LA). The main objective of this study was to develop a comprehensive understanding of the genomic epidemiology of HBOC throughout the establishment of The Latin American consortium for HBOC-LACAM, consisting of specialists from 5 countries in LA and the description of the genomic results from the first phase of the study. Methods: We have recruited 403 individuals that fulfilled the criteria for HBOC from 11 health institutions of Argentina, Colombia, Guatemala, Mexico and Peru. A pilot cohort of 222 individuals was analyzed by NGS gene panels. One hundred forty-three genes were selected on the basis of their putative role in susceptibility to different hereditary cancers. Libraries were sequenced in MiSeq (Illumina, Inc.) and PGM (Ion Torrent-Thermo Fisher Scientific) platforms. Results: The overall prevalence of pathogenic variants was 17% (38/222); the distribution spanned 14 genes and varied by country. The highest relative prevalence of pathogenic variants was found in patients from Argentina (25%, 14/57), followed by Mexico (18%, 12/68), Guatemala (16%, 3/19), and Colombia (13%, 10/78). Pathogenic variants were found in BRCA1 (20%) and BRCA2 (29%) genes. Pathogenic variants were found in other 12 genes, including high and moderate risk genes such as MSH2, MSH6, MUTYH, and PALB2. Additional pathogenic variants were found in HBOC unrelated genes such as DCLRE1C, WRN, PDE11A, and PDGFB. Conclusion: In this first phase of the project, we recruited 403 individuals and evaluated the germline genetic alterations in an initial cohort of 222 patients among 4 countries. Our data show for the first time in LA the distribution of pathogenic variants in a broad set of cancer susceptibility genes in HBOC. Even though we used extended gene panels, there was still a high proportion of patients without any detectable pathogenic variant, which emphasizes the larger, unexplored genetic nature of the disease in these populations.

Comprehensive Analysis of Germline Variants in Mexican Patients with Hereditary Breast and Ovarian Cancer Susceptibility

Hereditary breast and ovarian cancer syndrome (HBOC) represents 5⁻10% of all patients with breast cancer and is associated with high-risk pathogenic alleles in BRCA1/2 genes, but only for 25% of cases. We aimed to find new pathogenic alleles in a panel of 143 cancer-predisposing genes in 300 Mexican cancer patients with suspicion of HBOC and 27 high-risk patients with a severe family history of cancer, using massive parallel sequencing. We found pathogenic variants in 23 genes, including BRCA1/2. In the group of cancer patients 15% (46/300) had a pathogenic variant; 11% (33/300) harbored variants with unknown clinical significance (VUS) and 74% (221/300) were negative. The high-risk group had 22% (6/27) of patients with pathogenic variants, 4% (1/27) had VUS and 74% (20/27) were negative. The most recurrent mutations were the Mexican founder deletion of exons 9-12 and the variant p.G228fs in BRCA1, each found in 5 of 17 patients with alterations in this gene. Rare VUS with potential impact at the protein level were found in 21 genes. Our results show for the first time in the Mexican population a higher contribution of pathogenic alleles in other susceptibility cancer genes (54%) than in BRCA1/2 (46%), highlighting the high locus heterogeneity of HBOC and the necessity of expanding genetic tests for this disease to include broader gene panels.

Contribution of S4 segments and S4-S5 linkers to the low-voltage activation properties of T-type CaV3.3 channels

Voltage-gated calcium channels contain four highly conserved transmembrane helices known as S4 segments that exhibit a positively charged residue every third position, and play the role of voltage sensing. Nonetheless, the activation range between high-voltage (HVA) and low-voltage (LVA) activated calcium channels is around 30–40 mV apart, despite the high level of amino acid similarity within their S4 segments. To investigate the contribution of S4 voltage sensors for the low-voltage activation characteristics of Ca_V3.3 channels we constructed chimeras by swapping S4 segments between this LVA channel and the HVA Ca_V1.2 channel. The substitution of S4 segment of Domain II in Ca_V3.3 by that of Ca_V1.2 (chimera IIS4C) induced a ~35 mV shift in the voltage-dependence of activation towards positive potentials, showing an I-V curve that almost overlaps with that of Ca_V1.2 channel. This HVA behavior induced by IIS4C chimera was accompanied by a 2-fold decrease in the voltage-dependence of channel gating. The IVS4 segment had also a strong effect in the voltage sensing of activation, while substitution of segments IS4 and IIIS4 moved the activation curve of Ca_V3.3 to more negative potentials. Swapping of IIS4 voltage sensor influenced additional properties of this channel such as steady-state inactivation, current decay, and deactivation. Notably, Domain I voltage sensor played a major role in preventing Ca_V3.3 channels to inactivate from closed states at extreme hyperpolarized potentials. Finally, site-directed mutagenesis in the Ca_V3.3 channel revealed a partial contribution of the S4-S5 linker of Domain II to LVA behavior, with synergic effects observed in double and triple mutations. These findings indicate that IIS4 and, to a lesser degree IVS4, voltage sensors are crucial in determining the LVA properties of Ca_V3.3 channels, although the accomplishment of this function involves the participation of other structural elements like S4-S5 linkers.