A 5' UTR Language Model for Decoding Untranslated Regions of mRNA and Function Predictions.

The 5' UTR, a regulatory region at the beginning of an mRNA molecule, plays a crucial role in regulating the translation process and impacts the protein expression level. Language models have showcased their effectiveness in decoding the functions of protein and genome sequences. Here, we introduced a language model for 5' UTR, which we refer to as the UTR-LM. The UTR-LM is pre-trained on endogenous 5' UTRs from multiple species and is further augmented with supervised information including secondary structure and minimum free energy. We fine-tuned the UTR-LM in a variety of downstream tasks. The model outperformed the best known benchmark by up to 5% for predicting the Mean Ribosome Loading, and by up to 8% for predicting the Translation Efficiency and the mRNA Expression Level. The model also applies to identifying unannotated Internal Ribosome Entry Sites within the untranslated region and improves the AUPR from 0.37 to 0.52 compared to the best baseline. Further, we designed a library of 211 novel 5' UTRs with high predicted values of translation efficiency and evaluated them via a wet-lab assay. Experiment results confirmed that our top designs achieved a 32.5% increase in protein production level relative to well-established 5' UTR optimized for therapeutics.

Efficient and multiplexed somatic genome editing with Cas12a mice.

Somatic genome editing in mouse models has increased our understanding of the in vivo effects of genetic alterations in areas ranging from neuroscience to cancer biology and beyond. However, existing models are limited in their ability to create multiple targeted edits. Thus, our understanding of the complex genetic interactions that underlie development, homeostasis, and disease remains incomplete. Cas12a is an RNA-guided endonuclease with unique attributes that enable simple targeting of multiple genes with crRNA arrays containing tandem guides. To accelerate and expand the generation of complex genotypes in somatic cells, we generated transgenic mice with Cre-regulated and constitutive expression of enhanced Acidaminococcus sp. Cas12a (enAsCas12a). In these mice, enAsCas12a-mediated somatic genome editing robustly generated compound genotypes, as exemplified by the initiation of diverse cancer types driven by homozygous inactivation of trios of tumor suppressor genes. We further integrated these modular crRNA arrays with clonal barcoding to quantify the size and number of tumors with each array, as well as the efficiency of each crRNA. These Cas12a alleles will enable the rapid generation of disease models and broadly facilitate the high-throughput investigation of coincident genomic alterations in somatic cells in vivo .

The Outcome of the Miniaturized Percutaneous Nephrolithotomy in Lateral Position with Guidance of Non-Rotational C-Arm.

Objective: Evaluation of the outcome of the miniaturized percutaneous nephrolithotomy in the treatment of nephrolithiasis with a lateral position based on the principle of a right triangle under the guidance of a C-Arm without contrast fluid. Materials and Methods: Sixty-nine cases of Mini-PCNL with the assistance of a vacuum-assisted sheath in the lateral position were performed at Central Hospital from March 2021 to August 2022. Percutaneous renal access was under the guidance of a non-rotational C-arm without contrast medium, and we determined the puncture location and depth of the needle based on the principle of right triangles. Results: The median age was 51.6 ± 12.5 years, and males accounted for 68.1% of the cases. 60.9% of all patients had normal weight. The median stone surface area was 361.1mm2, and 59.4% of all cases were graded as 2 regarding Guy's stone score. The successful renal access rate was 100%. The tunnel access from the middle and lower calyx accounted for 94.2%. The median access duration, fluoroscopy duration, and hospital length of stay were 271.7 seconds, 14.79 seconds, and 6.3 days, respectively. The complete stone clearance rate was 78.3%. Bleeding complications occurred in 2 patients without mortality. Three patients required an additional procedure. Conclusion: The puncture technique into the renal calyxes based on the principle of the right triangle under the guidance of a non-rotational C-Arm without contrast medium in PCNL is a fast, exact, and safe technique.

Three-Dimensional Laparoscopic Nephrectomy for Benign Nonfunctioning Kidneys: A Single-Center Initial Experience.

BACKGROUND: There are several types of benign renal diseases, such as urological stones, ureteropelvic junction obstruction, renal vascular disease, and inflammation, which are responsible for nonfunctioning kidneys. Laparoscopic nephrectomy (LN) is the gold standard for treating nonfunctioning kidneys with complications. This study presents the results of our initial experiences with 3D laparoscopic nephrectomy (3D-LN) for benign, nonfunctioning kidneys. METHODS: From July 2021 to July 2023, 40 consecutive patients who underwent 3D transperitoneal laparoscopic nephrectomy were retrospectively evaluated at the Department of Urology and Department of General Surgery, Hue Central Hospital, Hue, Vietnam. Patient demographics, intraoperative and early postoperative results, postoperative recovery, complications, and three-month follow-up results were recorded. RESULTS: The mean age was 58.35 ± 14.9 years. There were 13 (32.5%) male and 27 (67.5%) female patients. Flank pain was the main reason for hospitalization in 33 cases (82.5%); the common cause of a nonfunctioning kidney was urological stones (62.5%). Twenty-three out of 40 patients underwent a left nephrectomy. The average operative time was 92.57 ± 28.69 minutes. A statistically significant difference in surgery time was found between the group with no adhesion and the group with mild adhesion, as well as between the first 19 patients and the last 18 patients (p <0.05). The mean blood loss was 51.62 ± 24.35 ml. Three cases were converted to open surgery due to severe adhesions. The postoperative complications rate was 8.1%. The average length of the postoperative hospital stay was 7.89 ± 3.59 days. CONCLUSIONS: Three-dimensional laparoscopic nephrectomy is a safe and effective method that increases depth perception and spatial orientation for surgeons and can compensate for the remaining shortcomings of traditional 2D systems.

APOE loss-of-function variants: Compatible with longevity and associated with resistance to Alzheimer's disease pathology.

The ε4 allele of apolipoprotein E (APOE) is the strongest genetic risk factor for sporadic Alzheimer's disease (AD). Knockdown of ε4 may provide a therapeutic strategy for AD, but the effect of APOE loss of function (LoF) on AD pathogenesis is unknown. We searched for APOE LoF variants in a large cohort of controls and patients with AD and identified seven heterozygote carriers of APOE LoF variants. Five carriers were controls (aged 71-90 years), one carrier was affected by progressive supranuclear palsy, and one carrier was affected by AD with an unremarkable age at onset of 75 years. Two APOE ε3/ε4 controls carried a stop-gain affecting ε4: one was cognitively normal at 90 years and had no neuritic plaques at autopsy; the other was cognitively healthy at 79 years, and lumbar puncture at 76 years showed normal levels of amyloid. These results suggest that ε4 drives AD risk through the gain of abnormal function and support ε4 knockdown as a viable therapeutic option.

Long sequence insertion via CRISPR/Cas gene-editing with transposase, recombinase, and integrase.

CRISPR/Cas-based gene-editing technologies have emerged as one of the most transformative tools in genome science over the past decade, providing unprecedented possibilities for both fundamental and translational research. Following the initial wave of innovations for gene knock-out, epigenetic/RNA modulation, and nickase-mediated base-editing, recent efforts have pivoted towards long-sequence gene editing- specifically, the insertion of large fragments (>1 kb) into the endogenous genome. In this review, we survey the development of these CRISPR/Cas-based sequence insertion methodologies in conjunction with the emergence of novel families of editing enzymes, such as transposases, single-stranded DNA-annealing proteins, recombinases, and integrases. Despite facing a number of challenges, this field continues to evolve rapidly and holds the potential to catalyze a new wave of revolutionary biomedical applications.