High Mutation Research Articles

Single-cell and Spatial Transcriptomic Analyses Implicate Formation of the Immunosuppressive Microenvironment during Breast Tumor Progression.

Ductal carcinoma in situ and invasive ductal carcinoma represent two stages of breast cancer progression. A multitude of studies have shown that genomic instability increases during tumor development, as manifested by higher mutation and copy number variation rates. The advent of single-cell and spatial transcriptomics has enabled the investigation of the subtle differences in cellular states during the tumor progression at single-cell level, thereby providing more nuanced understanding of the intercellular interactions within the solid tumor. However, the evolutionary trajectory of tumor cells and the establishment of the immunosuppressive microenvironment during breast cancer progression remain unclear. In this study, we performed an exploratory analysis of the single-cell sequencing dataset of 13 ductal carcinoma in situ and invasive ductal carcinoma samples. We revealed that tumor cells became more malignant and aggressive during their progression, and T cells transited to an exhausted state. The tumor cells expressed various coinhibitory ligands that interacted with the receptors of immune cells to create an immunosuppressive tumor microenvironment. Furthermore, spatial transcriptomics data confirmed the spatial colocalization of tumor and immune cells, as well as the expression of the coinhibitory ligand-receptor pairs. Our analysis provides insights into the cellular and molecular mechanism underlying the formation of the immunosuppressive landscape during two typical stages of breast cancer progression.

Population genomics of seal lice provides insights into the postglacial history of northern European seals.

Genetic analyses of host-specific parasites can elucidate the evolutionary histories and biological features of their hosts. Here, we used population-genomic analyses of ectoparasitic seal lice (Echinophthirius horridus) to shed light on the postglacial history of seals in the Arctic Ocean and the Baltic Sea region. One key question was the enigmatic origin of relict landlocked ringed seal populations in lakes Saimaa and Ladoga in northern Europe. We found that that lice of four postglacially diverged subspecies of the ringed seal (Pusa hispida) and Baltic gray seal (Halichoerus grypus), like their hosts, form genetically differentiated entities. Using coalescent-based demographic inference, we show that the sequence of divergences of the louse populations is consistent with the geological history of lake formation. In addition, local effective population sizes of the lice are generally proportional to the census sizes of their respective seal host populations. Genome-based reconstructions of long-term effective population sizes revealed clear differences among louse populations associated with gray versus ringed seals, with apparent links to Pleistocene and Holocene climatic variation as well as to the isolation histories of ringed seal subspecies. Interestingly, our analyses also revealed ancient gene flow between the lice of Baltic gray and ringed seals, suggesting that the distributions of Baltic seals overlapped to a greater extent in the past than is the case today. Taken together, our results demonstrate how genomic information from specialized parasites with higher mutation and substitution rates than their hosts can potentially illuminate finer scale population genetic patterns than similar data from their hosts.

Enhancing cisplatin drug sensitivity through PARP3 inhibition: The influence on PDGF and G-coupled signal pathways in cancer

Drug resistance poses a significant challenge in cancer treatment despite the clinical efficacy of cisplatin. Identifying and targeting biomarkers open new ways to improve therapeutic outcomes. In this study, comprehensive bioinformatic analyses were employed, including a comparative analysis of multiple datasets, to evaluate overall survival and mutation hotspots in 27 base excision repair (BER) genes of more than 7,500 tumors across 23 cancer types.By using various parameters influencing patient survival, revealing that the overexpression of 15 distinct BER genes, particularly PARP3, NEIL3, and TDG, consistently correlated with poorer survival across multiple factors such as race, gender, and metastasis. Single nucleotide polymorphism (SNP) analyses within protein-coding regions highlighted the potential deleterious effects of mutations on protein structure and function. The investigation of mutation hotspots in BER proteins identified PARP3 due to its high mutation frequency.Moving from bioinformatics to wet lab experiments, cytotoxic experiments demonstrated that the absence of PARP3 by CRISPR/Cas9-mediated knockdown in MDA-MB-231 breast cancer cells increased drug activity towards cisplatin, carboplatin, and doxorubicin. Pathway analyses indicated the impact of PARP3 absence on the platelet-derived growth factor (PDGF) and G-coupled signal pathways on cisplatin exposure.PDGF, a critical regulator of various cellular functions, was downregulated in the absence of PARP3, suggesting a role in cancer progression. Moreover, the influence of PARP3 knockdown on G protein-coupled receptors (GPCRs) affects their function in the presence of cisplatin.In conclusion, the study demonstrated a synthetic lethal interaction between GPCRs, PDGF signaling pathways, and PARP3 gene silencing. PARP3 emerged as a promising target.

Contrasting PRRSV temporal lineage patterns at the individual farm, production system, and regional levels in Ohio and neighboring states from 2017 to 2021

Porcine reproductive and respiratory virus (PRRSV), one of the most significant viruses in the swine industry, has been challenging to control due to its high mutation and recombination rates and complexity. This retrospective study aimed to describe and compare the distribution of PRRSV lineages obtained at the individual farm, production system, and regional levels. PRRSV-2 (type 2) sequences (n = 482) identified between 2017 – 2021 were provided by a regional state laboratory (Ohio Department of Agriculture, Animal Disease Diagnostic Center (ODA-ADDL)) collected from swine farms in Ohio and neighboring states, including Indiana, Michigan, Pennsylvania, and West Virginia. Additional sequences (n = 138) were provided by one collaborating swine production system. The MUSCLE algorithm on Geneious Prime® was used to align the ORF5 region of PRRSV-2 sequences along with PRRSV live attenuated vaccine strains (n = 6) and lineage anchors (n = 169). Sequenced PRRSV-2 were assigned to the most identical lineage anchors/vaccine strains. Among all sequences (n = 620), 29.8% (185/620) were ≥ 98.0% identity with the vaccine strains, where 93.5% (173/185) and 6.5% (12/185) were identical with the L5 Ingelvac PRRS® MLV and L8 Fostera® PRRS vaccine strains, respectively, and excluded from the analysis. At the regional level across five years, the top five most identified lineages included L1A, L5, L1H, L1C, and L8. Among non-vaccine sequences with production system known, L1A sequences were mostly identified (64.3% – 100.0%) in five systems, followed by L1H (0.0% - 28.6%), L1C (0.0% – 10.5%), L5 (0.0% – 14.4%), L8 (0.0% – 1.3%), and L1F (0.0% – 0.5%). Furthermore, among non-vaccine sequences with the premise identification available (n = 262), the majority of sequences from five individual farms were either classified into L1A or L5. L1A and L5 sequences coexisted in three farms, while samples submitted by one farm contained L1A, L1H, and L5 sequences. Additionally, the lineage classification results of non-vaccine sequences were associated with their restriction fragment length polymorphism (RFLP) patterns (Fisher’s exact test, p < 0.05). Overall, our results show that individual farm and production system-level PRRSV-2 lineage patterns do not necessarily correspond to regional-level patterns, highlighting the influence of individual farms and systems in shaping PRRSV occurrence within those levels, and highlighting the crucial goal of within-farm and system monitoring and early detection for accurate knowledge on PRRSV-2 lineage occurrence and emergence.

Phase II study of nivolumab in patients with genetic alterations in DNA damage repair and response who progressed after standard treatment for metastatic solid cancers (KM-06)

BackgroundImmune-modulating antibodies targeting programmed cell death protein 1/programmed death-ligand 1 (PD-1/PD-L1) have demonstrated promising antitumor efficacy in various types of cancers, especially highly mutated ones. Genetic alterations in DNA damage...

Molecular dynamics simulations show how antibodies may rescue HIV-1 mutants incapable of infecting host cells

High mutation and replication rates of HIV-1 result in the continuous generation of variants, allowing it to adapt to changing host environments. Mutations often have deleterious effects, but variants carrying them are rapidly purged. Surprisingly, a particular variant incapable of entering host cells was found to be rescued by host antibodies targeting HIV-1. Understanding the molecular mechanism of this rescue is important to develop and improve antibody-based therapies. To unravel the underlying mechanisms, we performed fully atomistic molecular dynamics simulations of the HIV-1 gp41 trimer responsible for viral entry into host cells, its entry-deficient variant, and its complex with the rescuing antibody. We find that the Q563R mutation, which the entry-deficient variant carries, prevents the native conformation of the gp41 6-helix bundle required for entry and stabilizes an alternative conformation instead. This is the consequence of substantial changes in the secondary structure and interactions between the domains of gp41. Binding of the antibody F240 to gp41 reverses these changes and re-establishes the native conformation, resulting in rescue. To test the generality of this mechanism, we performed simulations with the entry-deficient L565A variant and antibody 3D6. We find that 3D6 binding was able to reverse structural and interaction changes introduced by the mutation and restore the native gp41 conformation. Viral variants may not only escape antibodies but be aided by them in their survival, potentially compromising antibody-based therapies, including vaccination and passive immunization. Our simulation framework could serve as a tool to assess the likelihood of such resistance against specific antibodies. Communicated by Ramaswamy H. Sarma Communicated by Ramaswamy H. Sarma

High Frequency Mutant Genes and Prognosis Value of HIV-Related Diffuse Large B-Cell Lymphoma

Background: Diffuse large B-cell lymphoma (DLBCL) is the most common subtype in AIDS-related lymphoma (ARL) in HIV-infected patients, and the probability of DLBCL in HIV-infected patients is up to 17 times higher than that of the healthy population. However, the genetic mutation profile of HIV-associated DLBCL is still controversial, and the gene regulatory mechanism of HIV infection leading to the high incidence of DLBCL is still unclear. Methods: A total of 12 HIV-positiveDLBCL and 39 HIV-negativeDLBCL patients who treated in Chongqing University Cancer Hospital from March 2022 to October 2022 were enrolled. Tumor tissue samples were selected to detect by second-generation sequencing technology, and gene heat mapping was used to analyze the high-frequency mutant genes in HIV-positive lymphoma patients, comparing the differences mutant genes between HIV-positive and HIV-negative DLBCL patients. The specific mutant genes in HIV-positive DLBCL were screened, and Kaplan-Meier estimate the impact of specific gene changes on disease prognosis in analyze DLBCL lymphoma. Results Compared with HIV-negative DLBCL patients, 12 patients with HIV-positive DLBCL were mostly male (91.7%), and the disease subtype was mostly germinal center B-cell like(GCB) subtype (75%). HIV-positive DLBCL patients were associated with EBV infection, elevated LDH, increased proportion of CD4 + cells &amp;lt; 200 (cell/ul), and more aggressive. The gene heat mapping results showed that TP53, TBL1XR1 and KMT2D had higher mutations in HIV-positive DLBCL and HIV-negative DLBCL patients. Compared with HIV-positive DLBCL, HIV-negative DLBCL patients were more likely to have gene mutations such as IGLL5, KMT2C, CD79B, BTG1, HIST1H1E, TNFRSF14, B2M. Compared with HIV-negative DLBCL patients, HIV-positive DLBCL patients detected more complex gene mutation sites, and were more common to have gene mutations including TP53, LRP1B, MYC, NOTCH2, SPEN, EP300, SOCS1, TYK2, ARID1A, GNA13, MAP2K1. Among those gene mutations, LRP1B, MYC, TYK2 have a higher probability in HIV-positive DLBCL patients (P&amp;lt;0.05). Compared with HIV-negative DLBCL patients, HIV-positive DLBCL patients have a worse prognosis by Kaplan-Meier analysis, and patients with LRP1B, MYC, TYK2 mutations had a longer time to achieve complete remission. Conclusion HIV-positive DLBCL patients are more prone to gene mutations, and the mutant genes are more complex and diverse. LRP1B, MYC and TYK2 gene mutations may play an important role in the occurrence and development of HIV-positive DLBCL and affect the prognosis of patients. Keyword HIV; lymphoma; genetic mutation; prognosis

Genetic Characterization of the H Gene of MeV Strains (H1, B3, and D4) Recently Circulated in Iran for Improving the Molecular Measles Surveillance in the National Measles Lab.

Despite decreasing the global burden of measles disease after the introduction of vaccination, measles remains one of the most devastating childhood diseases. Since genotype B3 is reported as a predominant Measles Virus (MeV) genotype recently, the current study aimed to better understand MeV genetic variation by analyzing the complete sequence of Hemagglutinin (H) gene associated with outbreaks of circulated genotypes in Iran. Nine positive measles specimens were selected from three circulated different genotypes H1, B3, and D4. Two different regions of MeV RNA were detected by RT-PCR assay. Sequence data and phylogenetic trees were analyzed and constructed by MEGA X software program. Moreover, missense and silent mutations in critical positions of the MeV-H protein were investigated. The result of phylogenetic analysis from the C-terminus of the Nucleoprotein gene (NP-450) and the complete H gene revealed that the mean sequence diversity was 0.06%-0.08% and 0.04%, respectively. Genotype H1 had the highest mutation in this study; however, the substitutions in genotype B3 fundamentally occurred in critical epitopes. Moreover, genotype D4 was more stable than genotypes B3 and H1. Mutations were investigated in the whole sequence of H protein. Moreover, the mutations that occur in the critical sites of the protein have an important effect on the pathogenicity of the virus. In this way, we were able to illustrate why genotype B3 is more transmissible than other measles genotypes and is the most important circulating genotype around the world.

Utility of next generation sequencing (NGS) in advanced malignancies in a community hospital in an underserved area: A game changer?

e15037 Background: Next Generation Sequencing (NGS) is a revolutionary test used in advanced malignancies to study specific mutations, define tumor burdens, &amp; design personalized treatment plans based on the target mutations. With this study, our aim is to highlight the role of NGS, especially in a community hospital &amp; emphasize on its implementation as a standard of care in advanced metastatic cancers. Methods: We retrospectively reviewed the charts of 51 patients after IRB approval, aged &gt; 18 years with no specific demographic restrictions, with advanced malignancies who had NGS at Mercy Catholic Medical Center, PA. Results: Of 51 patients, 25 were males &amp; 26 were females, 44 patients had positive results on NGS. 100 types of mutations were identified &amp; 338 mutations in total were found. Lung cancer had highest mutations (41.17%-21/51), followed by colon (25.49% - 13/51), breast, ovarian &amp; endometrium (13.72% 7/51), &amp; the rest comprised of GI malignancies &amp; prostate cancers. Of 100 mutations, 32% (32/100) had actionable targets &amp; received NGS directed chemoimmunotherapy, 22% (22/100) mutations had experimental chemo-immunotherapeutic drugs, &amp; 49% (49/100) had no specific NGS directed therapy actionable/target mutation. The most common (1,2,3) &amp; some rare mutations (4,5 and 6) with directed immunotherapy noted on NGS are listed in Table 1. Conclusions: As per our study, 86.27% of the sample size showed positive results on NGS. 32% of these mutations had NGS directed chemoimmunotherapy against these target mutations. In contrary to standard treatment regimens, a personalized treatment plan was developed for these patients, thereby curbing further progression &amp; improving survival in patients with advanced cancer. For example, a patient with stage IV colon cancer who was progressing on the standard treatment with FOLFOX (Folinic acid, flurouracil and oxaliplatin), was started on Ivosedenib, after undergoing NGS and showed marked improvement clinically and radiologically. 29 out of 43 guidelines for various malignancies established by National Comprehensive Cancer Network highlight the significance of NGS. With this study, our goal is to emphasize on the utility of NGS in patients with advanced cancer &amp; the need for it to be incorporated as the standard of care, in small &amp; mid-tier community hospitals, which would need a devised plan for its implementation. [Table: see text]

Genomic and molecular landscape of homologous recombination deficiency across multiple cancer types

Homologous recombination deficiency (HRD) causes faulty double-strand break repair and is a prevalent cause of tumorigenesis. However, the incidence of HRD and its clinical significance in pan-cancer patients remain unknown. Using computational analysis of Single-nucleotide polymorphism array data from 10,619 cancer patients, we demonstrate that HRD frequently occurs across multiple cancer types. Analysis of the pan-cancer cohort revealed that HRD is not only a biomarker for ovarian cancer and triple-negative breast cancer, but also has clinical prognostic value in numerous cancer types, including adrenocortical cancer and thymoma. We discovered that homologous recombination–related genes have a high mutation or deletion frequency. Pathway analysis shows HRD is positively correlated with the DNA damage response and the immune-related signaling pathways. Single cell RNA sequencing of tumor-infiltrating lymphocytes reveals a significantly higher proportion of exhausted T cells in HRD patients, indicating pre-existing immunity. Finally, HRD could be utilized to predict pan-cancer patients’ responses to Programmed cell death protein 1 immunotherapy. In summary, our work establishes a comprehensive map of HRD in pan-cancer. The findings have significant implications for expanding the scope of Poly ADP-ribose polymerase inhibitor therapy and, possibly, immunotherapy.

Current state-of-the-art review of nanotechnology-based therapeutics for viral pandemics: Special attention to COVID-19

AbstractOver the past two centuries, most pandemics have been caused by zoonotic RNA viruses with high mutation, infection, and transmission rates. Due to the importance of understanding the viruses’ role in establishing the latest outbreak pandemics, we briefly discuss their etiology, symptomatology, and epidemiology and then pay close attention to the latest chronic communicable disease, SARS-CoV-2. To date, there are no generally proven effective techniques in the diagnosis, treatment, and spread strategy of viral diseases, so there is a profound need to discover efficient technologies to address these issues. Nanotechnology can be a promising approach for designing more functional and potent therapeutics against coronavirus disease 2019 (COVID-19) and other viral diseases. Moreover, this review intends to summarize examples of nanostructures that play a role in preventing, diagnosing, and treating COVID-19 and be a comprehensive and helpful review by covering notable and vital applications of nanotechnology-based strategies for improving health and environmental sanitation.

Cross-variant proof predictive vaccine design based on SARS-CoV-2 spike protein using immunoinformatics approach

BackgroundCoronavirus Disease (COVID-19) is caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The SARS-CoV-2 virus is evolving continuously. The omicron variant of SARS-CoV-2 has the highest mutation in its spike protein, thus making the presently available vaccine ineffective or reducing its efficiency. Furthermore, the majority of the vaccines are constructed using a spike protein sequence from wild-type SARS-CoV-2. This raises the possibility of the virus evolving to the point where the vaccine's effectiveness is completely lost, even after booster doses. The study aims to develop a predictive vaccine as well as the epitopes for the updating of the vaccine sequences of currently available vaccines. In this study, following the immunoinformatics approach, predictive vaccine construction was done with the help of epitopes present on spike proteins of wild-type, delta, and omicron variants that encompass the majority of variants and possible new variants that arise from the combination of circulating variants.ResultsThe vaccine that was constructed was stable and immunogenic. The vaccine was constructed with the help of 18 B-cell epitopes, 5 MHC class I epitopes, and 6 MHC class II epitopes. The epitope conservancy analysis suggests that the vaccine will work for the previously known variant of concern. The vaccine bound to TLR4, TLR2, B-cell receptor chains A and B, and ACE2 receptors with a z score of − 1.4, − 1.7, − 1.4, − 1.7, and − 1.4, respectively, with a cluster size of 121 highest for the ACE2 receptor and 46 lowest for B-cell receptor chain A. The C-ImmSim simulation results indicate that the vaccine is generating both humoral and cell-mediated responses at a sufficient level throughout the month upon injection of the vaccine as an antigen.ConclusionThe study's findings indicate that the vaccine was both stable and immunogenic, providing a sufficient level of immunity. Following experimental validation, the vaccine can be used, and the epitopes can be employed for therapeutic purposes such as antibody synthesis.Graphical

Association between Polymorphism Locus rs7041 and rs4588 in VDBP Gene and Vitamin D Status with Mortality in Sepsis Patient

Vitamin D deficiency was associated with an increased mortality risk in patients with sepsis. Loci rs7041 and rs4588 polymorphisms of the Vitamin D Binding Protein (VDBP) gene receptor caused a significantly increased risk of vitamin D deficiency in subtropical countries (Yordania). Simultaneously, similar studies for the tropics (Indonesia) have not been found yet. This study aims to analyze the association between polymorphism locus rs7041 and rs4588 in the vitamin D binding receptor gene and vitamin D status with the mortality of sepsis patients. This study was an analytical observation type with a cohort design. The relationship between the two groups was analyzed using the chi-square test/fisher test. Mutant’s polymorphism locus rs7041 in not survived patients is more than survived (65.0% vs. 35.0%) with a p-value of 0,025. The mortality risk was 1.625 times (RR 1.625 95% CI 1.044 – 2.529). The mutant’s polymorphism locus rs4588 locus in not survived patients is more than survived (70.3% vs. 29.7%) with a p-value of 0,022. The mortality risk was 1.622 times (RR 1.622 95% CI 1.095 – 2.402). Polymorphism loci rs7041 and rs4588 in not survived sepsis patients were higher mutants than the wild type. The highest vitamin D deficiency occurred in the mutant locus rs4588 (55.5%), but it was not statistically significant p &gt; 0.05. There was an association between Loci rs7041 and rs4588 polymorphisms and mortality of sepsis patients. No association was between Loci rs7041 and rs4588 polymorphisms with vitamin D status and between vitamin D status and mortality of patients with sepsis. Keywords: polymorphism, rs7041, rs4588, vitamin D, vitamin D binding protein, mortality, sepsis. https://doi.org/10.55463/issn.1674-2974.50.2.15

Pan-carcinogenic analysis of Annexin A1 gene in human tumors: A bioinformatics study

Background: Annexin A1 (ANXA1) and cancer appear to be related, based on emerging cell-based or animal research, but pan-cancer analysis is lacking. Objective: By using bioinformatics, we will examine the expression characteristics of the ANXA1 gene in pan-cancers. Methods: In collaboration with TCGA and GEO database, ANXA1 gene was analyzed pan-cancer, and through gene expression analysis, survival analysis, gene variation, immune infiltration, and enrichment analysis, ANXA1 played a role in the pathogenesis of different tumors. Results: A significant correlation has been found between ANXA1 expression and prognosis in some patients with tumors. The expression level of ANXA1 was correlated with the pathological stage of head and neck squamous cell carcinoma (HNSC) and thyroid carcinoma (THCA). The survival rates are related to the expression level of ANXA1 in different tumors. There is a strong correlation between the expression of ANXA1 and immune cell infiltration in some tumors and patients with sarcoma (SARC) and uterine corpus endometrial carcinoma (UCEC) have a higher mutation and amplification rate for the ANXA1 gene. ANXA1 may participate in the occurrence and development of tumor through "proteoglycans in cancer" signal pathways. Conclusion: The ANXA1 gene is involved in the pathogenesis of multiple kinds of tumors, and the study of its pathogenic mechanism may be an effective approach to treating tumors.

Expression of gasdermin D in clear cell renal cell carcinoma and its effect on its biological function.

Clear cell renal cell carcinoma (ccRCC) is the most common type of renal cell carcinoma, which suffers from the lack of diagnosis and treatment methods, and many patients cannot be diagnosed at first time. Gasdermin D (GSDMD) is involved in inflammatory reactions and pyroptosis and is considered a potential therapeutic target. This paper's aim is to elucidate the expression of GSDMD in clear cell renal cell carcinoma and its value for treatment and prognosis, as well as its impact on the biological function of clear cell renal cell carcinoma. The Cancer Genome Atlas (TCGA) database was used to compare the expression of GSDMD in tumor and normal tissues, analyze its correlation with cancer stage and overall survival time, and establish receiver operating characteristic (ROC) curve, which was confirmed by the Gene Expression Omnibus (GEO) database and immunohistochemical staining of clinical samples and PCR and Western blotting (WB) of cell lines. The relationship between GSDMD and patient prognosis and staging was analyzed using TCGA database and validated using clinical sample data. Differentially expressed genes (DEGs) and epithelial-mesenchymal transition (EMT)-related genes of GSDMD were screened by TCGA database. Protein-protein interaction (PPI) of GSDMD was constructed by GeneMANIA and STRING, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment were analyzed by the Metascape database. Then, R software was used to analyze the immune cell infiltration, immune microenvironment score, and tumor mutational burden (TMB) analysis of GSDMD high- and low-expression groups in TCGA database. GSDMD lentivirus was used to transfect 769-P cells to construct stable upregulated and downregulated transfected cell lines. PCR was used to verify the expression differences of differentially expressed genes between the high- and low-expression groups of GSDMD; then, MTT, flow apoptosis, and Transwell were used to detect the proliferation, apoptosis, invasion, and migration of the transfected cells. The results of bioinformatics analysis showed that the expression of GSDMD in clear cell renal cell carcinoma was significantly correlated with patient stage and overall survival, and the tumor with high expression of GSDMD had a worse stage and overall survival. GSDMD has some significance in the diagnosis of ccRCC. The results of EMT correlation analysis and enrichment analysis showed that GSDMD was correlated with genes and pathways related to invasion and metastasis of renal cell carcinoma. The subsequent immune cell infiltration analysis showed that there were many differences in the infiltration of immune cells between the high- and low-expression groups of GSDMD, such as naive B cells. The immune microenvironment score showed that the high-expression group had a lower proportion of stromal cells than the local expression group but had a higher proportion of immune cells. Through TMB, it was shown that the high-expression group had a higher mutation. The expression of GSDMD in renal cell carcinoma by immunohistochemistry and in vitro cell experiments was confirmed. According to the prognostic information of clinical patients, it was found that GSDMD was significantly correlated with TNM stage, Fuhrman grade, lymph node metastasis, gender, and smoking or not, and the prognosis of patients with high expression of GSDMD was worse. After that, we constructed stable transfection cell lines with high expression and knockdown through lentivirus transfection and verified the expression amount of differentially expressed genes by PCR, which is consistent with the results of TCGA database. Then, we confirmed that GSDMD is related to proliferation, invasion, migration, and apoptosis of ccRCC by MTT, flow apoptosis, and Transwell assay. The low expression of GSDMD inhibits the proliferation, invasion, and migration of tumors and enhances apoptosis and vice versa. Therefore, GSDMD can be used as a potential biological marker for the diagnosis and prognosis of ccRCC.

Detection of High-Frequency Mutation Genes in HIV-Positive and HIV-Negative Lymphomas

Objective Compare HIV-positive lymphoma with HIV-negative lymphoma mutation genes differences, screen specific mutations genes in HIV-positive lymphoma, analyze high frequency mutation genes in HIV-positive lymphoma patients, and explore the effect of HIV infection on lymphoma gene mutation and disease development. It can provide a theoretical basis for the clincal diagnosis and targeted therapy HIV-positive lymphoma. Methods A total of 7 HIV-positive lymphoma patients and 13 HIV-negative lymphoma patients who were treated in Chongqing University Cancer Hospital from September 2020 to September 2021 were enrolled. Tumor tissue samples were detected by second-generation sequencing technology, and gene mutations in HIV-positive lymphoma patients were analyzed by gene heat map, comparing the gene mutation differences between HIV-positive and HIV-negative lymphoma patients. Results Compared with HIV-negative lymphoma patients, more and more complex gene mutation sites were detected in HIV-positive lymphoma patients. Single nucleotide mutation of MYC gene was more common in HIV-positive lymphoma patients, while deletion of KMT2D gene was more common in HIV-negative lymphoma patients. And TP53 gene is highly mutated in both HIV-positive and HIV-negative lymphoma patients. However, mutations of TET, CCND3, TNFRSF14, ARID1A, TNFAIP3, NFKBIE, CXCR4, STAT3, NOTCH1 and other gene mutation with low mutation abundency occurred only in HIV-positive lymphoma patients. NOTCH2, PRDM1, EZH2, CARD11, EP300, MEF2B, CREBBP and other gene mutations occurred only in HIV-negative lymphoma patients. Conclusion HIV-positive lymphoma patients are more prone to gene mutations, and the gene mutations are more complex and diverse. MYC gene mutations and TP53 gene mutations play an important role in the occurrence and development of HIV-positive lymphoma, while the occurrence and development of HIV-negative lymphoma are more related to KMT2D gene mutations and TP53 gene mutations.

Chromosomally Unstable Gastric Cancers Overexpressing Claudin-6 Disclose Cross-Talk between HNF1A and HNF4A, and Upregulated Cholesterol Metabolism.

(1) Abnormally increased expression of claudin-6 in gastric cancer is considered a prognostic marker of the chromosomal unstable molecular subtype. However, a detailed molecular profile analysis of differentially expressed genes and affected pathways associated with claudin-6 increased (Cldn6high) expression has not been assessed. (2) The TCGA Stomach Adenocarcinoma Pan-Cancer Atlas Data was evaluated using Cytoscape's Gene Mania, MCODE, and Cytohubba bioinformatic software. (3) 96.88% of Cldn6high gastric cancer tumors belonging to the chromosomal unstable molecular subtype are associated with a worse prognosis. Cldn6expression coincided with higher mutations in TP53, MIEN1, STARD3, PGAP3, and CCNE1 genes compared to Cldn6low expression. In Cldn6high cancers, 1316 genes were highly expressed. Cholesterol metabolism was the most affected pathway as APOA1, APOA2, APOH, APOC2, APOC3, APOB-100, LDL receptor-related protein 1/2, Sterol O-acyltransferase, STARD3, MAGEA-2, -3, -4, -6, -9B, and -12 genes were overexpressed in Cldn6high gastric cancers; interestingly, APOA2 and MAGEA9b were identified as top hub genes. Functional enrichment of DEGs linked HNF-4α and HNF-1α genes as highly expressed in Cldn6high gastric cancer. (4) Our results suggest that APOA2 and MAGEA9b could be considered as prognostic markers for Cldn6high gastric cancers.

Circulating and Salivary NGF and BDNF Levels in SARS-CoV-2 Infection: Potential Predictor Biomarkers of COVID-19 Disease-Preliminary Data.

COVID-19 continues to afflict the global population, causing several pathological diseases and exacerbating co-morbidities due to SARS-CoV-2's high mutation. Recent interest has been devoted to some neuronal manifestations and to increased levels of Nerve Growth Factor (NGF) and Brain-derived Neurotrophic Factor (BDNF) in the bloodstream during SARS-CoV-2 infection, neurotrophins that are well-known for their multifactorial actions on neuro-immune-endocrine and visual functions. Nineteen (19) patients were enrolled in this monocentric prospective study and subjected to anamnesis and biosamples collection (saliva and blood) at hospitalization (acute phase) and 6 months later (remission phase). NGF and BDNF were quantified by ELISA, and biochemical data were related to biostrumental measurements. Increased NGF and BDNF levels were quantified in saliva and serum during the acute phase of SARS-CoV-2 infection (hospitalized patients), and reduced levels were observed in the next 6 months (remission phase), never matching the baseline values. Salivary and circulating data would suggest the possibility of considering sera and saliva as useful matrices for quickly screening neurotrophins, in addition to SARS-CoV2 antigens and RNA. Overall, the findings described herein highlight the importance of NGF and BDNF as dynamic biomarkers for monitoring disease and reinforces the possibility of using saliva and sera for quick, non-invasive COVID-19 screening.

Identification of Potential ACE2-Derived Peptide Mimetics in SARS-CoV-2 Omicron Variant Therapeutics using Computational Approaches.

The COVID-19 pandemic has become a global health challenge because of the emergence of distinct variants. Omicron, a new variant, is recognized as a variant of concern (VOC) by the World Health Organization (WHO) because of its higher mutations and accelerated human infection. The infection rate is strongly dependent on the binding rate of the receptor binding domain (RBD) against human angiotensin converting enzyme-2 (ACE2human) receptor. Inhibition of protein–protein (RBDs(SARS-CoV-2/omicron)-ACE2human) interaction has been already proven to inhibit viral infection. We have systematically designed ACE2human-derived peptides and peptide mimetics that have high binding affinity toward RBDomicron. Our peptide mutational analysis indicated the influence of canonical amino acids on the peptide binding process. Herein, efforts have been made to explore the atomistic details and events of RBDs(SARS-CoV-2/omicron)-ACE2human interactions by using molecular dynamics simulation. Our studies pave a path for developing therapeutic peptidomimetics against omicron.

Relationship between ATOH1 and tumor microenvironment in colon adenocarcinoma patients with different microsatellite instability status

BackgroundColon adenocarcinoma (COAD) is one of the major varieties of malignant tumors threatening human health today. Immune checkpoint inhibitors (ICIs) have recently begun to emerge as an effective option for the treatment of COAD patients, but not all patients can benefit from ICI treatment. Previous studies have suggested that ICIs boast significant clinical effects on patients with microsatellite instability-high (MSI-H), while conversely patients with microsatellite-stable/microsatellite instability-low (MSS/MSI-L) have shown limited response.MethodsWe used ATAC-seq, RNA-seq, and mutation data from The Cancer Genome Atlas Colon adenocarcinoma (TCGA-COAD) cohort to perform multi-omics differential analysis on COAD samples with different MSI statuses, then further screened genes by additionally combining these results with survival analysis. We analyzed the effects of the screened genes on the tumor microenvironment and immunogenicity of COAD patients, and subsequently determined their influence on the efficacy of ICIs in COAD patients using a series of predictive indexes.ResultsTwelve genes were screened in the TCGA-COAD cohort, and after the combined survival analysis, we identified ATOH1 as having significant effects. ATOH1 is characterized by high chromatin accessibility, high expression, and high mutation in COAD patients in the MSI-H group. COAD patients with high ATOH1 expression are associated with a better prognosis, unique immune microenvironment, and higher efficacy in ICI treatment. Enrichment analysis showed that COAD patients with high ATOH1 expression displayed significant upregulation in their humoral immunity and other related pathways.ConclusionsWe speculate that ATOH1 may influence the efficacy of ICIs therapy in patients with COAD by affecting the immune microenvironment and immunogenicity of the tumor.