Bioinformatics. 2024 Sep 3:btae531. doi: 10.1093/bioinformatics/btae531. Online ahead of print.

ABSTRACT

MOTIVATION: Systems biology analyses often use correlations in gene expression profiles to infer co-expression networks that are then used as input for gene regulatory network inference or to identify functional modules of co-expressed or putatively co-regulated genes. While systematic biases, including batch effects, are known to induce spurious associations and confound differential gene expression analyses (DE), the impact of batch effects on gene co-expression has not been fully explored. Methods have been developed to adjust expression values, ensuring conditional independence of mean and variance from batch or other covariates for each gene, resulting in improved fidelity of DE analysis. However, such adjustments do not address the potential for spurious differential co-expression (DC) between groups. Consequently, uncorrected, artifactual DC can skew the correlation structure, leading to the identification of false, non-biological associations, even when the input data is corrected using standard batch correction.

RESULTS: In this work, we demonstrate the persistence of confounders in covariance after standard batch correction using synthetic and real-world gene expression data examples. We then introduce Co-expression Batch Reduction Adjustment (COBRA), a method for computing a batch-corrected gene co-expression matrix based on estimating a conditional covariance matrix. COBRA estimates a reduced set of parameters expressing the co-expression matrix as a function of the sample covariates, allowing control for continuous and categorical covariates. COBRA is computationally efficient, leveraging the inherently modular structure of genomic data to estimate accurate gene regulatory associations and facilitate functional analysis for high-dimensional genomic data.

AVAILABILITY AND IMPLEMENTATION: COBRA is available under the GLP3 open source license in R and Python in netZoo (https://netzoo.github.io).

SUPPLEMENTARY INFORMATION: Supplementary information is available at Bioinformatics online.

PMID:39226186 | DOI:10.1093/bioinformatics/btae531

Hepatol Commun. 2024 Sep 3;8(9):e0494. doi: 10.1097/HC9.0000000000000494. eCollection 2024 Sep 1.

ABSTRACT

BACKGROUND: Primary sclerosing cholangitis (PSC) is associated with biliary obstructions that can require endoscopic retrograde cholangiopancreatography (ERCP). While the beneficial effects of ERCP are well documented, follow-up interventional strategies are less defined, and their long-term impact is debated.

METHODS: We evaluated the outcome of a scheduled program of ERCP-guided interventions that have been developed and implemented at our tertiary liver center for more than 20 years. Within our center, follow-up ERCPs were performed at regular intervals to treat previously detected morphological stenosis independent of clinical symptoms. We calculated the transplant-free survival (TFS) of patients who were enrolled in the scheduled ERCP program and compared it to patients who received follow-up ERCPs only on clinical demand. Moreover, we documented the occurrence of hepatic decompensation, recurrent cholangitis episodes, hepatobiliary malignancies, and endoscopy-related adverse events.

RESULTS: In our retrospective study, we included 201 patients with PSC who all received an ERCP. In all, 133 patients received scheduled follow-up ERCPs and 68 received follow-up ERCPs only on demand. The rates of TFS since initial diagnosis (median TFS: 17 vs. 27 y; P = 0.020) and initial presentation (median TFS: 16 vs. 11 y; P = 0.002) were higher in patients receiving scheduled versus on-demand ERCP. Subgroup analysis revealed that progression in cholangiographic findings between the first and second ERCP was associated with a poorer outcome compared to patients without progression (17 y vs. undefined; P = 0.021).

CONCLUSION: In conclusion, we report the outcome data of a scheduled follow-up ERCP program for patients with PSC in an experienced high-volume endoscopy center. Our data suggest the initiation of multicenter randomized controlled prospective trials to explore the full potential of regular endoscopic follow-up treatment as a strategy to prevent disease progression in patients with PSC.

PMID:39225697 | DOI:10.1097/HC9.0000000000000494

Front Oncol. 2024 Aug 19;14:1419599. doi: 10.3389/fonc.2024.1419599. eCollection 2024.

ABSTRACT

Cancer therapy is facing increasingly significant challenges, marked by a wide range of techniques and research efforts centered around somatic mutations, precision oncology, and the vast amount of big data. Despite this abundance of information, the quest to cure cancer often seems more elusive, with the "war on cancer" yet to deliver a definitive victory. A particularly pressing issue is the development of tumor treatment resistance, highlighting the urgent need for innovative approaches. Evolutionary, Quantum Biology and System Biology offer a promising framework for advancing experimental cancer research. By integrating theoretical studies, translational methods, and flexible multidisciplinary clinical research, there's potential to enhance current treatment strategies and improve outcomes for cancer patients. Establishing stronger links between evolutionary, quantum, entropy and chaos principles and oncology could lead to more effective treatments that leverage an understanding of the tumor's evolutionary dynamics, paving the way for novel methods to control and mitigate cancer. Achieving these objectives necessitates a commitment to multidisciplinary and interprofessional collaboration at the heart of both research and clinical endeavors in oncology. This entails dismantling silos between disciplines, encouraging open communication and data sharing, and integrating diverse viewpoints and expertise from the outset of research projects. Being receptive to new scientific discoveries and responsive to how patients react to treatments is also crucial. Such strategies are key to keeping the field of oncology at the forefront of effective cancer management, ensuring patients receive the most personalized and effective care. Ultimately, this approach aims to push the boundaries of cancer understanding, treating it as a manageable chronic condition, aiming to extend life expectancy and enhance patient quality of life.

PMID:39224803 | PMC:PMC11367711 | DOI:10.3389/fonc.2024.1419599

Adv Biomed Res. 2024 Jul 29;13:42. doi: 10.4103/abr.abr_229_23. eCollection 2024.

ABSTRACT

BACKGROUND: Celiac disease (CeD) is an autoimmune enteropathy triggered by dietary gluten. Almost 90% of CeD patients have HLA-DQ2 or -DQ8 haplotypes. As a high proportion of first-degree relatives (FDRs) of CeD patients have the same haplotype, it is assumed that they are at a higher risk of disease development than the general population. Nevertheless, the prevalence of CeD among FDRs is considerably low (7.5%).

MATERIALS AND METHODS: In order to figure out this discrepancy, a microarray dataset of intestinal mucosal biopsies of CeD patients, FDRs, and control groups was reanalyzed, and a protein-protein interaction network was constructed.

RESULTS: Principal component analysis showed that CeD and FDR groups are far away in terms of gene expression. Comparing differentially expressed genes of both networks demonstrated inverse expression of some genes mainly related to cell cycle mechanisms. Moreover, analysis of the modular structures of up- and downregulated gene networks determined activation of protein degradation mechanisms and inhibition of ribosome-related protein synthesis in celiac patients with an upside-down pattern in FDRs.

CONCLUSIONS: The top-down systems biology approach determined some regulatory pathways with inverse function in CeD and FDR groups. These genes and molecular mechanisms could be a matter of investigation as potential druggable targets or prognostic markers in CeD.

PMID:39224401 | PMC:PMC11368239 | DOI:10.4103/abr.abr_229_23

Front Microbiol. 2024 Aug 19;15:1421749. doi: 10.3389/fmicb.2024.1421749. eCollection 2024.

ABSTRACT

Pyoverdines are high affinity siderophores produced by most Pseudomonas with a wide role in microbial interspecies interactions. They are primarily composed of a conserved chromophore moiety, an acyl side chain and a peptide backbone which may be highly variable among strains. Upon ferric iron sequestration, pyoverdines are internalized through specialized receptors. The peptide precursor of pyoverdine, termed ferribactin, is synthesized by a set of non-ribosomal peptide synthetase (NRPS) enzymes and further modified by tailoring enzymes. While PvdL, the NRPS responsible for the synthesis of the peptide moiety that derives into the chromophore is conserved, the NRPSs for the peptide backbone are different across fluorescent Pseudomonas. Although the variation of pyoverdine is a widely recognized characteristic within the genus, the evolutionary events associated with the diversity and distribution of this trait remain mostly unknown. This study analyzed the NRPSs clusters for the biosynthesis of the peptide backbone of ferribactin in the genomes of a representative subset of strains of the Pseudomonas fluorescens complex. Bioinformatic analysis of the specificity of adenylation domains of the NRPSs allowed the prediction of 30 different pyoverdine variants. Phylogenetic reconstruction and mapping of the NRPS clusters pinpointed two different general levels of modifications. In the first level, a complete replacement of the set of NRPRs by horizontal transfer occurs. In the second level, the original set of NRPSs is modified through different mechanisms, including partial substitution of the NRPS genes by horizontal transfer, adenylation domain specificity change or NRPS accessory domain gain/loss.

PMID:39224222 | PMC:PMC11366639 | DOI:10.3389/fmicb.2024.1421749

BMC Plant Biol. 2024 Sep 3;24(1):823. doi: 10.1186/s12870-024-05553-z.

ABSTRACT

BACKGROUND: DNA methylation is a critical factor influencing plant growth, adaptability, and phenotypic plasticity. While extensively studied in model and crop species, it remains relatively unexplored in holm oak and other non-domesticated forest trees. This study conducts a comprehensive in-silico mining of DNA methyltransferase and demethylase genes within the holm oak genome to enhance our understanding of this essential process in these understudied species. The expression levels of these genes in adult and seedling leaves, as well as embryos, were analysed using quantitative real-time PCR (qRT-PCR). Global DNA methylation patterns were assessed through methylation-sensitive amplified polymorphism (MSAP) techniques. Furthermore, specific methylated genomic sequences were identified via MSAP sequencing (MSAP-Seq).

RESULT: A total of 13 DNA methyltransferase and three demethylase genes were revealed in the holm oak genome. Expression levels of these genes varied significantly between organs and developmental stages. MSAP analyses revealed a predominance of epigenetic over genetic variation among organs and developmental stages, with significantly higher global DNA methylation levels observed in adult leaves. Embryos exhibited frequent demethylation events, while de novo methylation was prevalent in seedling leaves. Approximately 35% of the genomic sequences identified by MSAP-Seq were methylated, predominantly affecting nuclear genes and intergenic regions, as opposed to repetitive sequences and chloroplast genes. Methylation was found to be more pronounced in the exonic regions of nuclear genes compared to their promoter and intronic regions. The methylated genes were predominantly associated with crucial biological processes such as photosynthesis, ATP synthesis-coupled electron transport, and defence response.

CONCLUSION: This study opens a new research direction in analysing variability in holm oak by evaluating the epigenetic events and mechanisms based on DNA methylation. It sheds light on the enzymatic machinery governing DNA (de)methylation, and the changes in the expression levels of methylases and demethylases in different organs along the developmental stages. The expression level was correlated with the DNA methylation pattern observed, showing the prevalence of de novo methylation and demethylation events in seedlings and embryos, respectively. Several methylated genes involved in the regulation of transposable element silencing, lipid biosynthesis, growth and development, and response to biotic and abiotic stresses are highlighted. MSAP-seq integrated with whole genome bisulphite sequencing and advanced sequencing technologies, such as PacBio or Nanopore, will bring light on epigenetic mechanisms regulating the expression of specific genes and its correlation with the phenotypic variability and the differences in the response to environmental cues, especially those related to climate change.

PMID:39223458 | DOI:10.1186/s12870-024-05553-z

EMBO Rep. 2024 Sep 2. doi: 10.1038/s44319-024-00234-2. Online ahead of print.

ABSTRACT

Dinoflagellates, a class of unicellular eukaryotic phytoplankton, exhibit minimal transcriptional regulation, representing a unique model for exploring gene expression. The biosynthesis, distribution, regulation, and function of mRNA N1-methyladenosine (m1A) remain controversial due to its limited presence in typical eukaryotic mRNA. This study provides a comprehensive map of m1A in dinoflagellate mRNA and shows that m1A, rather than N6-methyladenosine (m6A), is the most prevalent internal mRNA modification in various dinoflagellate species, with an asymmetric distribution along mature transcripts. In Amphidinium carterae, we identify 6549 m1A sites characterized by a non-tRNA T-loop-like sequence motif within the transcripts of 3196 genes, many of which are involved in regulating carbon and nitrogen metabolism. Enriched within 3'UTRs, dinoflagellate mRNA m1A levels negatively correlate with translation efficiency. Nitrogen depletion further decreases mRNA m1A levels. Our data suggest that distinctive patterns of m1A modification might influence the expression of metabolism-related genes through translational control.

PMID:39223385 | DOI:10.1038/s44319-024-00234-2

Nat Cell Biol. 2024 Sep 2. doi: 10.1038/s41556-024-01492-x. Online ahead of print.

NO ABSTRACT

PMID:39223372 | DOI:10.1038/s41556-024-01492-x

Nat Genet. 2024 Sep 2. doi: 10.1038/s41588-024-01880-x. Online ahead of print.

ABSTRACT

Inhibiting epigenetic modulators can transcriptionally reactivate transposable elements (TEs). These TE transcripts often generate unique peptides that can serve as immunogenic antigens for immunotherapy. Here, we ask whether TEs activated by epigenetic therapy could appreciably increase the antigen repertoire in glioblastoma, an aggressive brain cancer with low mutation and neoantigen burden. We treated patient-derived primary glioblastoma stem cell lines, an astrocyte cell line and primary fibroblast cell lines with epigenetic drugs, and identified treatment-induced, TE-derived transcripts that are preferentially expressed in cancer cells. We verified that these transcripts could produce human leukocyte antigen class I-presented antigens using liquid chromatography with tandem mass spectrometry pulldown experiments. Importantly, many TEs were also transcribed, even in proliferating nontumor cell lines, after epigenetic therapy, which suggests that targeted strategies like CRISPR-mediated activation could minimize potential side effects of activating unwanted genomic regions. The results highlight both the need for caution and the promise of future translational efforts in harnessing treatment-induced TE-derived antigens for targeted immunotherapy.

PMID:39223316 | DOI:10.1038/s41588-024-01880-x

Ann Hematol. 2024 Sep 3. doi: 10.1007/s00277-024-05763-3. Online ahead of print.

ABSTRACT

BACKGROUND: Acute lymphoblastic leukemia (ALL) is a common hematologic cancer with unique incidence and prognosis patterns in people of all ages. Recent molecular biology advances have illuminated ALL's complex molecular pathways, notably the Hedgehog (Hh) signaling system and non-coding RNAs (ncRNAs). This work aimed to unravel the molecular complexities of the link between Hh signaling and ALL by concentrating on long non-coding RNAs (lncRNAs) and their interactions with significant Hh pathway genes.

METHODS: To analyze differentially expressed lncRNAs and genes in ALL, microarray data from the Gene Expression Omnibus (GEO) was reanalyzed using a systems biology approach. Hh signaling pathway-related genes were identified and their relationship with differentially expressed long non-coding RNAs (DElncRNAs) was analyzed using Pearson's correlation analysis. A regulatory network was built by identifying miRNAs that target Hh signaling pathway-related mRNAs.

RESULTS: 193 DEGs and 226 DElncRNAs were found between ALL and normal bone marrow samples. Notably, DEGs associated with the Hh signaling pathway were correlated to 26 DElncRNAs. Later studies showed interesting links between DElncRNAs and biological processes and pathways, including drug resistance, immune system control, and carcinogenic characteristics. DEGs associated with the Hh signaling pathway have miRNAs in common with miRNAs already known to be involved in ALL, including miR-155-5p, and miR-211, highlighting the complexity of the regulatory landscape in this disease.

CONCLUSION: The complex connections between Hh signaling, lncRNAs, and miRNAs in ALL have been unveiled in this study, indicating that DElncRNAs linked to Hh signaling pathway genes could potentially serve as therapeutic targets and diagnostic biomarkers for ALL.

PMID:39223285 | DOI:10.1007/s00277-024-05763-3

Schizophrenia (Heidelb). 2024 Sep 2;10(1):75. doi: 10.1038/s41537-024-00497-7.

ABSTRACT

Growing evidence suggests a potential link between the gut microbiome and schizophrenia. However, it is unclear whether the gut microbiome is causally associated with schizophrenia. We performed two-sample bidirectional Mendelian randomization to detect bidirectional causal relationships between gut microbiome and schizophrenia. Summary genome-wide association study (GWAS) datasets of the gut microbiome from the MiBioGen consortium (n = 18,340) and schizophrenia (n = 130,644) were utilized in our study. Then a cohort of sensitive analyses was followed to validate the robustness of MR results. We identified nine taxa that exerted positive causal effects on schizophrenia (OR: 1.08-1.16) and six taxa that conferred negative causal effects on schizophrenia (OR: 0.88-0.94). On the other hand, the reverse MR analysis showed that schizophrenia may increase the abundance of nine taxa (OR: 1.03-1.08) and reduce the abundance of two taxa (OR: 0.94). Our study unveiled mutual causal relationships between gut microbiome and schizophrenia. The findings may provide evidence for the treatment potential of gut microbiomes in schizophrenia.

PMID:39223235 | DOI:10.1038/s41537-024-00497-7

Eur J Vasc Endovasc Surg. 2024 Aug 31:S1078-5884(24)00789-5. doi: 10.1016/j.ejvs.2024.08.044. Online ahead of print.

NO ABSTRACT

PMID:39222772 | DOI:10.1016/j.ejvs.2024.08.044

Brief Bioinform. 2024 Jul 25;25(5):bbae424. doi: 10.1093/bib/bbae424.

ABSTRACT

Accurate taxonomic profiling of microbial taxa in a metagenomic sample is vital to gain insights into microbial ecology. Recent advancements in sequencing technologies have contributed tremendously toward understanding these microbes at species resolution through a whole shotgun metagenomic approach. In this study, we developed a new bioinformatics tool, coverage-based analysis for identification of microbiome (CAIM), for accurate taxonomic classification and quantification within both long- and short-read metagenomic samples using an alignment-based method. CAIM depends on two different containment techniques to identify species in metagenomic samples using their genome coverage information to filter out false positives rather than the traditional approach of relative abundance. In addition, we propose a nucleotide-count-based abundance estimation, which yield lesser root mean square error than the traditional read-count approach. We evaluated the performance of CAIM on 28 metagenomic mock communities and 2 synthetic datasets by comparing it with other top-performing tools. CAIM maintained a consistently good performance across datasets in identifying microbial taxa and in estimating relative abundances than other tools. CAIM was then applied to a real dataset sequenced on both Nanopore (with and without amplification) and Illumina sequencing platforms and found high similarity of taxonomic profiles between the sequencing platforms. Lastly, CAIM was applied to fecal shotgun metagenomic datasets of 232 colorectal cancer patients and 229 controls obtained from 4 different countries and 44 primary liver cancer patients and 76 controls. The predictive performance of models using the genome-coverage cutoff was better than those using the relative-abundance cutoffs in discriminating colorectal cancer and primary liver cancer patients from healthy controls with a highly confident species markers.

PMID:39222062 | DOI:10.1093/bib/bbae424

Elife. 2024 Sep 2;13:e99263. doi: 10.7554/eLife.99263. Online ahead of print.

ABSTRACT

The initially homogeneous epithelium of the early Drosophila embryo differentiates into regional subpopulations with different behaviours and physical properties that are needed for morphogenesis. The factors at top of the genetic hierarchy that control these behaviours are known, but many of their targets are not. To understand how proteins work together to mediate differential cellular activities, we studied in an unbiased manner the proteomes and phosphoproteomes of the three main cell populations along the dorso-ventral axis during gastrulation using mutant embryos that represent the different populations. We detected 6111 protein groups and 6259 phosphosites of which 3398 and 3433 respectively, were differentially regulated. The changes in phosphosite abundance did not correlate with changes in host protein abundance, showing phosphorylation to be a regulatory step during gastrulation. Hierarchical clustering of protein groups and phosphosites identified clusters that contain known fate determinants such as Doc1, Sog, Snail and Twist. The recovery of the appropriate known marker proteins in each of the different mutants we used validated the approach, but also revealed that two mutations that both interfere with the dorsal fate pathway, Toll10B and serpin27aex do this in very different manners. Diffused network analyses within each cluster point to microtubule components as one of the main groups of regulated proteins. Functional studies on the role of microtubules provide the proof of principle that microtubules have different functions in different domains along the DV axis of the embryo.

PMID:39221782 | DOI:10.7554/eLife.99263

Front Pharmacol. 2024 Aug 16;15:1447283. doi: 10.3389/fphar.2024.1447283. eCollection 2024.

ABSTRACT

Background: Stephania tetrandra has been used for treating rheumatic diseases for thousands of years in rural areas of China. Several studies have found that tetrandrine and fangchinoline can inactivate the PI3K/Akt signaling pathway by reducing the expression and phosphorylation of AKT. However, the mechanism underlying the therapeutic actions of S. tetrandra on RA is not well known. Methods: In this study, we determined the molecular mechanism of the therapeutic effects of the multiple ingredients of S. tetrandra extract (STE) on collagen-induced arthritic (CIA) rats by integrating pharmacometabolomics, proteomics, and PTMomics. Results: In the multi-omics joint analysis, first, the expression signatures of proteins, PTMs, metabolites, and STE ingredients were profiled in CIA rats PBMCs that underwent STE treatment. Bioinformatics analysis were subsequently probed that STE mainly regulated tryptophan metabolism, inflammatory response, and cell adhesion pathways in CIA rats. The interrelated pathways were further constructed, and the findings revealed that STE attenuated the inflammatory response and proliferation of PBMCs in CIA rats by mediating the key targets of the PI3K/Akt pathway, including Hint1, ACP1, FGR, HSP90@157W + dioxidation, and Prkca@220N + 845.4540 Da. The rheumatic functions of Hint1 and ACP1 were further confirmed by applying a transcriptomic data of RA patients who clinically received abatacept therapy. Furthermore, a cross-ome correlation analysis was performed and major in vivo ingredients of STE, including coclaurine-N-glucuronide, Me,coclaurine-O-glc, N-gluA-schefferine, corydamine, corypamine, tetrandrine, and fangchiniline, were found to act on these targerts to inactivate the PI3K/Akt pathway. Conclusion: These results elucidated the molecular mechanism by which the ingredients of STE mediate the expression of the key targets in the PI3K/Akt pathway, leading to anti-rheumatic functions. The findings of this study provided new insights into the synergistic effect of STE against arthritis in rats.

PMID:39221139 | PMC:PMC11361992 | DOI:10.3389/fphar.2024.1447283

Int J Cardiol Heart Vasc. 2024 Aug 7;54:101483. doi: 10.1016/j.ijcha.2024.101483. eCollection 2024 Oct.

ABSTRACT

BACKGROUND: Monoclonal antibodies (mAbs) are currently under investigation as a potential therapeutic option for COVID-19. Clinical trials are examining their efficacy in lowering mortality rates and the requirement for mechanical ventilation (MV). It is necessary to conduct a thorough examination of current randomized controlled trials (RCTs) in order to provide more definitive evidence on their effectiveness for COVID-19 patients. This meta-analysis aims to analyze RCT results on the impact of three mAbs (Anakinra, Sarilumab, Tocilizumab) on COVID-19 patient outcomes.

METHOD: The meta-analysis was conducted in accordance with the PRISMA guidelines. Eligible RCTs were conducted to evaluate the effectiveness of three mAbs in treating patients with COVID-19. These trials were identified by searching various databases up to April 1, 2024. In total, this meta-analysis incorporated 19 trials with a total of 8097 patients. Pooled relative risk and studies' heterogeneity were assessed by statistical analysis, which involved the use of fixed effects models and subgroup analysis.

RESULT: The administration of mAbs (Tocilizumab, Sarilumab, and Anakinra) showed various results in the management of COVID-19 patients. While the overall pooled data did not reveal a significant reduction in the need for MV, the study found that the use of mAbs was associated with a decreased risk of clinical worsening (pooled relative risk: 0.75, 95 % CI [0.59, 0.94], p = 0.01) and an increased probability of discharging COVID-19 patients by day 28 or 29 (pooled relative risk: 1.17, 95 % CI [1.10, 1.26]). Notably, the subgroup analysis revealed that Tocilizumab had a significant effect in reducing the risk of clinical worsening compared to Sarilumab. Additionally, the analysis of mortality outcomes indicated that the administration of mAbs had the potential to decrease the overall risk of mortality over time (pooled RR: 0.90, 95 % CI [0.83, 0.97], p = 0.01).

CONCLUSION: In summary, our meta-analysis suggests that mAbs, particularly Tocilizumab, may play a valuable role in managing COVID-19 by reducing the risk of clinical worsening, improving hospital discharge rates, and decreasing mortality.

PMID:39221116 | PMC:PMC11363488 | DOI:10.1016/j.ijcha.2024.101483

ACS Cent Sci. 2024 Jul 22;10(8):1442-1459. doi: 10.1021/acscentsci.4c00642. eCollection 2024 Aug 28.

ABSTRACT

Limited understanding of human proteoforms with complex posttranslational modifications and the underlying mechanisms poses a major obstacle to research on human health and disease. This Outlook discusses opportunities and challenges of de novo chemical protein synthesis in human proteoform studies. Our analysis suggests that to develop a comprehensive, robust, and cost-effective methodology for chemical synthesis of various human proteoforms, new chemistries of the following types need to be developed: (1) easy-to-use peptide ligation chemistries allowing more efficient de novo synthesis of protein structural domains, (2) robust temporary structural support strategies for ligation and folding of challenging targets, and (3) efficient transpeptidative protein domain-domain ligation methods for multidomain proteins. Our analysis also indicates that accurate chemical synthesis of human proteoforms can be applied to the following aspects of biomedical research: (1) dissection and reconstitution of the proteoform interaction networks, (2) structural mechanism elucidation and functional analysis of human proteoform complexes, and (3) development and evaluation of drugs targeting human proteoforms. Overall, we suggest that through integrating chemical protein synthesis with in vivo functional analysis, mechanistic biochemistry, and drug development, synthetic chemistry would play a pivotal role in human proteoform research and facilitate the development of precision diagnostics and therapeutics.

PMID:39220697 | PMC:PMC11363345 | DOI:10.1021/acscentsci.4c00642

Anim Cells Syst (Seoul). 2024 Aug 29;28(1):417-427. doi: 10.1080/19768354.2024.2393811. eCollection 2024.

ABSTRACT

Calcium ions (Ca2+) play pivotal roles in regulating numerous cellular functions, including metabolism and growth, in normal and cancerous cells. Consequently, Ca2+ signaling is a vital determinant of cell fate and influences both cell survival and death. These intracellular signals are susceptible to modulation by various factors, including changes in the extracellular environment, which leads to mechanical alterations. However, the effect of extracellular matrix (ECM) stiffness variations on intracellular Ca2+ signaling remains underexplored. In this study, we aimed to elucidate the mechanisms of Ca2+ regulation through the mitochondria, which are crucial to Ca2+ homeostasis. We investigated how Ca2+ regulatory mechanisms adapt to different levels of ECM stiffness by simultaneously imaging the mitochondria and endoplasmic reticulum (ER) in live cells using genetically encoded biosensors. Our findings revealed that the uptake of mitochondrial Ca2+ through Voltage-Dependent Anion Channel 1 (VDAC1), facilitated by intracellular tubulin, is influenced by ECM stiffness. Unraveling these Ca2+ regulatory mechanisms under various conditions offers a novel perspective for advancing biomedical studies involving Ca2+ signaling.

PMID:39220629 | PMC:PMC11363740 | DOI:10.1080/19768354.2024.2393811

F1000Res. 2024 Jul 30;13:481. doi: 10.12688/f1000research.150684.2. eCollection 2024.

ABSTRACT

Protein-glutamine gamma-glutamyltransferase 2 (TGM2) is a Ca 2+ dependent enzyme that catalyzes transglutaminase cross-linking modifications. TGM2 is involved in various diseases, either in a protective or contributory manner, making it a crucial protein to study and determine its therapeutic potential. Identifying high-performing TGM2 antibodies would facilitate these investigations. Here we have characterized seventeen TGM2 commercial antibodies for western blot and sixteen for immunoprecipitation, and immunofluorescence. The implemented standardized experimental protocol is based on comparing read-outs in knockout cell lines against their isogenic parental controls. This study is part of a larger, collaborative initiative seeking to address antibody reproducibility issues by characterizing commercially available antibodies for human proteins and publishing the results openly as a resource for the scientific community. While the use of antibodies and protocols vary between laboratories, we encourage readers to use this report as a guide to select the most appropriate antibodies for their specific needs.

PMID:39220380 | PMC:PMC11362715 | DOI:10.12688/f1000research.150684.2

Front Bioeng Biotechnol. 2024 Aug 16;12:1423935. doi: 10.3389/fbioe.2024.1423935. eCollection 2024.

ABSTRACT

Since their first industrial application in the acetone-butanol-ethanol (ABE) fermentation in the early 1900s, Clostridia have found large application in biomass biorefining. Overall, their fermentation products include organic acids (e.g., acetate, butyrate, lactate), short chain alcohols (e.g., ethanol, n-butanol, isobutanol), diols (e.g., 1,2-propanediol, 1,3-propanediol) and H2 which have several applications such as fuels, building block chemicals, solvents, food and cosmetic additives. Advantageously, several clostridial strains are able to use cheap feedstocks such as lignocellulosic biomass, food waste, glycerol or C1-gases (CO2, CO) which confer them additional potential as key players for the development of processes less dependent from fossil fuels and with reduced greenhouse gas emissions. The present review aims to provide a survey of research progress aimed at developing Clostridium-mediated biomass fermentation processes, especially as regards strain improvement by metabolic engineering.

PMID:39219620 | PMC:PMC11365079 | DOI:10.3389/fbioe.2024.1423935