Journal: Human Genetics and Genomics Advances

Article Title: Using a modular massively parallel reporter assay to discover context-dependent regulatory activity in type 2 diabetes-linked noncoding regions

doi: 10.1016/j.xhgg.2026.100606

Figure Lengend Snippet: HNF1 transcription factor motifs contribute to enhancer activity near selected T2D-associated variants (A) For 47 HNF1-motif-overlapping fragments with significant INS promoter-bias effects on activity, we designed three versions: original (motif intact), deleted (motif removed and sequence adjusted), and shuffled (dinucleotide-shuffled motif). When the tested variant was adjacent to the motif, we synthesized both reference and alternative alleles for each version. For variants directly overlapping the motif, we generated only one deletion and one shuffled fragment. (B) We synthesized four fragments corresponding to the variant rs1635852, which overlaps an HNF1 motif at a high-information-content position. The T2D risk allele (T) disrupts this motif, while the non-risk allele (C) matches the consensus. (C) Shuffling the motif significantly decreased enhancer activity compared to intact fragments with either the risk T (Wilcoxon rank-sum test p = 0.016) or non-risk C ( p = 0.008) allele. Motif deletion also significantly decreased enhancer activity compared to the non-risk C allele ( p = 0.016). (D) For the variant rs11819995, located 11 bp upstream of an HNF1 motif, we synthesized six fragments. (E) Deletion of the motif significantly decreased enhancer activity for both the reference (C, non-risk) and alternative (T, risk) alleles ( p = 0.008 for both alleles). Shuffling the motif likewise reduced activity for both alleles ( p = 0.008 for the reference allele and p = 0.056 for the alternative allele). (F) To assess context-specific effects, we cloned these fragments into MPRA vectors with the SCP1 or skeletal-muscle-specific MYBPC2 promoter and delivered all three to LHCN-M2 human skeletal muscle myotubes ( n = 6). (G) When paired with the INS promoter, the shuffled rs11819995-containing fragment showed increased activity relative to the original fragment ( p = 0.015); however, none of the fragments containing rs11819995 functioned as enhancers in LHCN-M2 myotubes, regardless of promoter context. Overall, their activity is highest when paired with the skeletal-muscle-specific promoter.

Article Snippet: We obtained INS-1 832/13 rat insulinoma cells from Dr. Christopher Newgard (Sarah W. Stedman Nutrition and Metabolism Center, Duke University, Durham, NC) and LHCN-M2 human skeletal muscle myoblasts from Evercyte.

Techniques: Activity Assay, Sequencing, Variant Assay, Synthesized, Generated, Clone Assay

Journal: Molecular Therapy. Nucleic Acids

Article Title: Single-base 2′OMe-modified LNA and MOE gapmers selectively silence ACVR1 R206H in fibrodysplasia ossificans progressiva

doi: 10.1016/j.omtn.2026.102937

Figure Lengend Snippet: Preferential silencing of ACVR1 R206H in FOP patient-derived fibroblasts using LNA and MOE gapmers (A) Sequence alignment showing LNA and MOE gapmer binding sites spanning the ACVR1 c.617G>A mutation (R206H). Mismatches are shown in lowercase; green: ACVR1 WT variant; red: ACVR1 R206H variant. (B) Schematic overview of the experimental timeline: day 2, cell revival; day 0, seeding; day 1, transfection; day 3, RNA/protein harvest. Toxicity assessments were performed at 4, 12, 24, and 48 h post-transfection. (C and D) RT-qPCR analysis of total ACVR1 mRNA levels following treatment with 100 nM (C) or 10 nM (D) gapmers. (E) Representative immunoblots showing total ACVR1 protein levels post-treatment with 100 and 10 nM gapmers. GAPDH served as a loading control. (F and G) Quantification of total ACVR1 protein abundance relative to healthy control cells at 100 nM (F) and 10 nM (G) using densitometric analysis of the immunoblot images (E). (H–K) Allele-specific RT-qPCR quantification of ACVR1 WT (H, J) and ACVR1 R206H (I, K) transcript levels following treatment with 100 nM (H, I) or 10 nM (J, K) gapmers. (L) Representative immunoblots of V5-tagged ACVR1 WT and ACVR1 R206H proteins expressed in C2C12 cells 48 h post-treatment with 10 nM gapmers, with GAPDH as a loading control. (M and N) Densitometric quantification of immunoblot images (L) showing V5-tagged ACVR1 WT (M) and ACVR1 R206H (N) protein levels in C2C12 cells relative to untreated controls. Statistics, one-way ANOVA with Tukey’s multiple comparisons test; ∗∗∗∗ p < 0.0001. Data are represented as mean ± standard error of the mean ( n = 5–7). NT, non-treated; Lipo, lipofectamine 3000 (a commercially available transfection reagent).

Article Snippet: Murine C2C12 myoblasts (American Type Culture Collection, VA, USA) were cultured in DMEM/F-12 medium supplemented with 15% FBS and 0.5% penicillin-streptomycin under standard conditions.

Techniques: Derivative Assay, Sequencing, Binding Assay, Mutagenesis, Variant Assay, Transfection, Quantitative RT-PCR, Western Blot, Control, Quantitative Proteomics

Journal: Molecular Therapy. Nucleic Acids

Article Title: Single-base 2′OMe-modified LNA and MOE gapmers selectively silence ACVR1 R206H in fibrodysplasia ossificans progressiva

doi: 10.1016/j.omtn.2026.102937

Figure Lengend Snippet: Single-base 2′OMe modification enhances allele selectivity and suppresses ACVR1 R206H -induced osteogenic differentiation in vitro (A and B) RT-qPCR quantification of ACVR1 WT (A) and ACVR1 R206H (B) transcripts in FOP patient-derived fibroblasts treated with 10 nM LNA16 or MOE3 gapmers, with or without a single 2′OMe modification at the second position of the gap region. (C) Allelic fractions of ACVR1 WT and ACVR1 R206H transcripts post-treatment as calculated from total ACVR1 expression. Green and red bars represent ACVR1 WT and ACVR1 R206H transcript fractions, respectively. (D and E) RT-qPCR quantification of ACVR1 WT (D) and ACVR1 R206H (E) transcripts in C2C12 myoblasts transfected with V5-tagged ACVR1 WT or ACVR1 R206H constructs and treated with 10 nM gapmers for 48 h. (F) Allelic fraction analysis of ACVR1 WT and ACVR1 R206H transcripts in cells from (D and E), similarly as (C). (G) Representative immunoblot showing V5-tagged ACVR1 WT and ACVR1 R206H protein levels in transfected C2C12 cells after 10 nM gapmer treatment. GAPDH served as a loading control. (H and I) Densitometric quantification of ACVR1 WT (H) and ACVR1 R206H (I) protein expression from (G), normalized to GAPDH and expressed relative to the non-treated control. (J) Representative images of alkaline phosphatase (ALP) staining in C2C12 cells expressing V5- ACVR1 R206H or ACVR1 WT , treated with 10 nM gapmers and stimulated with recombinant human activin A (100 ng/mL) for 48 h. (K) Quantification of secreted ALP enzymatic activity in conditioned media collected from cells in (J), normalized to the ACVR1 WT media. (L) Representative images of ARS staining performed 21 days after osteogenic differentiation induction in C2C12 cells transfected with V5- ACVR1 R206H or ACVR1 WT and treated with gapmers. (M) Quantification of ARS staining from (L), normalized to the ACVR1 WT control. Statistics, one-way ANOVA with Tukey’s multiple comparisons test; ∗ p < 0.05, ∗∗ p < 0.01, ∗∗∗∗ p < 0.0001. Scale bars, 250 μm. Data are represented as mean ± standard error of the mean ( n = 6–7). NT, non-treated; Lipo, lipofectamine 3000 (a commercially available transfection reagent).

Article Snippet: Murine C2C12 myoblasts (American Type Culture Collection, VA, USA) were cultured in DMEM/F-12 medium supplemented with 15% FBS and 0.5% penicillin-streptomycin under standard conditions.

Techniques: Modification, In Vitro, Quantitative RT-PCR, Derivative Assay, Expressing, Transfection, Construct, Western Blot, Control, Staining, Recombinant, Activity Assay