Journal: Molecular Therapy. Nucleic Acids

Article Title: Enhancing protein expression in humans through codon optimization with transformer and contrastive learning

doi: 10.1016/j.omtn.2026.102991

Figure Lengend Snippet: Experimental comparison of codon-optimized constructs in HEK293T cells (A) Western blot analysis of HEK293T cells transfected with wild-type or codon-optimized EMG1 , JNK1 , and CREB1 constructs generated by ExpOptimizer, GenSmart, or COformer. Protein expression was detected using an anti-His antibody, with GAPDH as a loading control. (B) Quantification of protein expression normalized to GAPDH and shown as fold change relative to wild-type. Data represent mean ± SD from three independent experiments. Statistical significance was assessed using one-way ANOVA followed by Tukey’s multiple comparison test. ∗ p < 0.05, ∗∗ p < 0.01 vs. wild-type; # p < 0.05, ## p < 0.01 vs. ExpOptimizer; & p < 0.05, && p < 0.01 vs. GenSmart. (C) Relative transcript abundance measured by RNA-seq 24 h post-transfection and normalized to GAPDH . Expression values are shown as fold change relative to wild type.

Article Snippet: Three micrograms of purified total RNA for each sample was shipped for genome-wide RNA sequencing (Plasmidsaurus).

Techniques: Comparison, Construct, Western Blot, Transfection, Generated, Expressing, Control, RNA Sequencing

Journal: Molecular Therapy. Nucleic Acids

Article Title: Enhancing protein expression in humans through codon optimization with transformer and contrastive learning

doi: 10.1016/j.omtn.2026.102991

Figure Lengend Snippet: Benchmarking COformer against commercial tools and learning-based models on a held-out test set COformer was compared with ExpOptimizer, GenSmart, GeneArt, ICOR, and CodonTransformer using identical held-out protein inputs. Sequence-level descriptors included (A) CAI, (B) overall GC fraction, (C) GC3 fraction, (D) uridine fraction, and (E) tAI. For (A–E), each distribution represents sequence-level values calculated for individual held-out protein inputs. Violin width reflects the density of observations, and internal lines indicate the 25th percentile, median, and 75th percentile. (F) Predicted RNA secondary-structure MFE was computed using ViennaRNA. For the boxplot, the center line indicates the median, the box spans the interquartile range, and whiskers extend to the most extreme values within 1.5 times the interquartile range.

Article Snippet: Three micrograms of purified total RNA for each sample was shipped for genome-wide RNA sequencing (Plasmidsaurus).

Techniques: Sequencing

Journal: Molecular therapy. Methods & clinical development

Article Title: PAM-altering SNP-based allele-specific CRISPR-Cas9 therapeutic strategies for Huntington's disease.

doi: 10.1016/j.omtm.2022.08.005

Figure Lengend Snippet: Figure 3. High levels of mutant HTT specificity supported by RNA-seq analysis Allele-specific expression (ASE) analysis was performed to evaluate the levels of allele specificity of our TP-CRISPR strategies. HD subjects with the most frequent diplotype (i.e., hap.01 and hap.08) are heterozygous at 10 exonic SNPs. Thus, we performed ASE using those 10 exonic SNP sites. Alleles of those 10 exonic SNPs on the mutant and normal HTT were based on our haplotype definitions and previous sequencing analysis. We counted the alleles on the mutant and normal HTT for a given SNP site, and then calculated average values. (A) Mean allele counts of 10 heterozygous exonic SNPs on the mutant HTT are summarized. Boxes on the left and right represent the distribution of alleles on the mutant HTT in EV-treated and targeted clonal lines, respectively. Student’s t test was performed (nominal p value, 3.53e6). (B) The same analysis approach was applied to alleles of 10 heterozygous exonic SNPs that are on the normal HTT. Boxes on the left and right represent the distribution of alleles in EV-treated and targeted clonal lines, respectively. Student’s t test was performed (nominal p value, 0.67). Each box shows maximum, 75%, 50% (median), 75% quartile, and minimum.

Article Snippet: Then, genome-wide RNA-seq analysis was performed by the Broad Institute.

Techniques: Mutagenesis, RNA Sequencing, Expressing, CRISPR, Sequencing

Journal: Molecular therapy. Methods & clinical development

Article Title: PAM-altering SNP-based allele-specific CRISPR-Cas9 therapeutic strategies for Huntington's disease.

doi: 10.1016/j.omtm.2022.08.005

Figure Lengend Snippet: Figure 4. On-target gene specificity supported by RNA-seq analysis To increase the sensitivity and the power to detect any small but significantly altered genes, we combined 10 targeted clonal lines targeted by L4-R4 and 10 clonal lines targeted by L4-R6 gRNA combinations to be compared with 12 EV-treated controls. (A) Significance values (un- corrected p values on the y axis) were compared with log2 (fold-change) (x axis) to highlight significantly altered genes. A horizontal and a vertical line represent Bonfer- roni-corrected significance and zero fold-change, respectively. (B) Expression levels of total HTT (mutant plus normal) based on the DGE analysis are summarized in a boxplot. Total HTT levels were decreased by 38% in TP-CRISPR targeted clonal lines.

Article Snippet: Then, genome-wide RNA-seq analysis was performed by the Broad Institute.

Techniques: RNA Sequencing, Expressing, Mutagenesis, CRISPR