Journal: Nature

Article Title: In vivo site-specific engineering to reprogram T cells

doi: 10.1038/s41586-026-10235-x

Figure Lengend Snippet: a , Tumour challenge schematic for multiple myeloma. NSG MHC-I/II double-KO mice received i.v. OPM2 cells (1 × 10 6 ), followed 5 days later by human PBMCs (1 × 10 7 ). Then, 5 days after PBMC transfer, mice received PBS or anti-CD3-EDV (5 × 10 11 sgRNAs per mouse; Cas9–sgTRAC) plus AAV-hT7 (1 × 10 12 vg per mouse), delivering a TRAC HDRT encoding a BCMA-1XX-CAR-P2A-EGFRt. The tumour burden was monitored using BLI. At day 35 after EDV/AAV treatment, mice were rechallenged i.v. with OPM2 cells (5 × 10 6 ). b , BLI measurements in mice injected with OPM2 alone ( n = 5), OPM2 + PBMC ( n = 8) or OPM2 + PBMC + EDV/AAV ( n = 8). Rechallenge was performed in four EDV/AAV-treated mice that controlled tumour growth by day 35 and in five age-matched control mice. BLI values represent the mean of dorsal and ventral signals (photons per s per cm 2 ). c , Tumour challenge schematic for solid tumours. NSG MHC-I/II double-KO mice received subcutaneous (s.c.) MES-SA cells (4 × 10 6 ), followed 4 days later by human PBMCs (1 × 10 7 ). Then, 3 days after PBMC transfer, mice received PBS or anti-CD3-EDV (5 × 10 11 sgRNAs per mouse) plus AAV-hT7 (1 × 10 12 vg per mouse), delivering a TRAC HDRT encoding an anti-B7H3-CD28ζ-1XX-CAR-P2A-EGFRt. The tumour burden was assessed by calliper measurements. d , Kaplan–Meier survival analysis of mice bearing MES-SA tumours; MES-SA only ( n = 4), MES-SA + PBMC ( n = 5) or MES-SA + PBMC + EDV/AAV (anti-B7H3–CD28ζ−1XX TRAC CAR; n = 6). e , Tumour growth measurements from the mice in d . CR, complete response. Images in a and c were adapted from Servier Medical Art ( https://smart.servier.com/ ), under a CC BY 4.0 licence.

Article Snippet: MES-SA cells (ATCC, CRL-1976) were cultured in McCoy’s 5a modified medium (Gibco, 16600082) supplemented with 10% FBS and penicillin–streptomycin.

Techniques: Injection, Control

Journal: Nature

Article Title: In vivo site-specific engineering to reprogram T cells

doi: 10.1038/s41586-026-10235-x

Figure Lengend Snippet: a , Dorsal images from mice described in Fig. . BLI is displayed as radiance (p/sec/cm 2 /sr). Days are indicated from time of PBS or EDV/AAV treatment. Day 11, 14, 21, 28 ans 35 are shown with and without mice that are saturating the signal. b , Total body weight from mice in Fig. . c , Experimental conditions from Fig. were repeated with an additional PBMC donor. Kaplan-Meier survival analysis in mice injected with MES-SA only (n = 4), MES-SA and PBMC (n = 5), MES-SA, PBMC and EDV/AAV targeting a aB7H3-CD28z-1XX (n = 6) CAR to TRAC . d , Tumour measurements in mice injected with MES-SA only (n = 4), MES-SA and PBMC (n = 5), MES-SA, PBMC and EDV/AAV targeting a aB7H3-CD28z-1XX (n = 8) CAR to TRAC . e , Total body weight from mice in c , d .

Article Snippet: MES-SA cells (ATCC, CRL-1976) were cultured in McCoy’s 5a modified medium (Gibco, 16600082) supplemented with 10% FBS and penicillin–streptomycin.

Techniques: Injection

Journal: bioRxiv

Article Title: A genome language model for mapping DNA replication origins

doi: 10.64898/2026.01.29.702604

Figure Lengend Snippet: a) Heatmaps of Spearman correlation across combinations of probability- and efficiency-smoothing windows in H1, illustrating genome-wide sensitivity to resolution matching. b) Dependence of the Spearman correlation on smoothing-window size for multiple species/cell types (H1, mESC, and sheep fibroblast), plotted as mean ± standard deviation across autosomes, highlighting cross-species consistency.

Article Snippet: Chicken embryonic fibroblast cells (UMNSAH/DF-1) were purchased from ATCC (ATCC-CRL-3586) and were maintained according to the supplier’s instructions in DMEM (ATCC 30-2002) supplemented with 10% fetal bovine serum (Gibco, 10270-106).

Techniques: Genome Wide, Standard Deviation

Journal: bioRxiv

Article Title: A genome language model for mapping DNA replication origins

doi: 10.64898/2026.01.29.702604

Figure Lengend Snippet: a) Schematic representation of ORILINX training on human origins of replication sequences, followed by applying ORILINX predictions in chicken, sheep and mouse without additional adjustments. b) ROC curves showing the ORILINX model performance in 28,490 SNS-seq chicken embryonic fibroblast cell origins of replication and matched number of random non-origin sequences, resulting in an AUC ROC = 0.92 and AUC PR =0.93. c) Same as in b) but for 79,574 SNS-seq sheep primary fibroblast origins and matched number random non-origin sequences from two replicates, resulting in an AUC ROC = 0.93 and AUC PR = 0.94. d) Same as in b) and c) but for publicly available mouse ESC data of 13,004 SNS-seq origins and matched number of random non-origin sequences, resulting in an AUC ROC = 0.81 and AUC PR = 0.85.

Article Snippet: Chicken embryonic fibroblast cells (UMNSAH/DF-1) were purchased from ATCC (ATCC-CRL-3586) and were maintained according to the supplier’s instructions in DMEM (ATCC 30-2002) supplemented with 10% fetal bovine serum (Gibco, 10270-106).

Techniques:

Journal: bioRxiv

Article Title: A genome language model for mapping DNA replication origins

doi: 10.64898/2026.01.29.702604

Figure Lengend Snippet: AUC ROC and AUC PR curves for individual SNS-seq replicates of the sheep fibroblast cells (see Methods). a) Replicate 1 showed an AUC ROC of 0.93 and AUC PR of 0.94. b) Replicate 2 showed an AUC ROC of 0.94 and AUC PR of 0.95.

Article Snippet: Chicken embryonic fibroblast cells (UMNSAH/DF-1) were purchased from ATCC (ATCC-CRL-3586) and were maintained according to the supplier’s instructions in DMEM (ATCC 30-2002) supplemented with 10% fetal bovine serum (Gibco, 10270-106).

Techniques:

Journal: bioRxiv

Article Title: A genome language model for mapping DNA replication origins

doi: 10.64898/2026.01.29.702604

Figure Lengend Snippet: Correlation analyses for a) sheep primary fibroblast, where Spearman’s ρ = 0.81, p-value ≪ 0.0001, and b) mouse embryonic stem cells (mESC), where Spearman’s ρ = 0.78, p-value ≪ 0.0001. For each species, the left panel shows chromosome 1 profiles comparing ORILINX predicted origin probability (red) with origin efficiency inferred from replication timing data (blue), with both signals smoothed using a 10 Mb moving average window. Spearman correlation coefficients are indicated. The right panel shows the corresponding joint density distributions of origin probability and origin efficiency computed genome-wide.

Article Snippet: Chicken embryonic fibroblast cells (UMNSAH/DF-1) were purchased from ATCC (ATCC-CRL-3586) and were maintained according to the supplier’s instructions in DMEM (ATCC 30-2002) supplemented with 10% fetal bovine serum (Gibco, 10270-106).

Techniques: Genome Wide