Xalud Therapeutics (United States)

Abstract The rapid expansion of massively parallel sequencing technologies has enabled the development of foundation models to uncover novel biological findings. While these have the potential to significantly accelerate scientific discoveries by creating AI-driven virtual cell models, their progress has been greatly limited by the lack of large-scale high-quality perturbation data, which remains constrained due to scalability bottlenecks and assay variability. Here, we introduce “Fix-Cryopreserve-ScRNAseq” (FiCS) Perturb-seq, an industrialized platform for scalable Perturb-seq data generation. We demonstrate that FiCS Perturb-seq exhibits high sensitivity and low batch effects, effectively capturing perturbation-induced transcriptomic changes and recapitulating known biological pathways and protein complexes. In addition, we release X-Atlas: Orion edition (X-Atlas/Orion), the largest publicly available Perturb-seq atlas. This atlas, generated from two genome-wide FiCS Perturb-seq experiments targeting all human protein-coding genes, comprises eight million cells deeply sequenced to over 16,000 unique molecular identifiers (UMIs) per cell. Furthermore, we show that single guide RNA (sgRNA) abundance can serve as a proxy for gene knockdown (KD) efficacy. Leveraging the deep sequencing and substantial cell numbers per perturbation, we also show that stratification by sgRNA expression can reveal dose-dependent genetic effects. Taken together, we demonstrate that FiCS Perturb-seq is an efficient and scalable platform for high-throughput Perturb-seq screens. Through the release of X-Atlas/Orion, we highlight the potential of FiCS Perturb-seq to address current scalability and variability challenges in data generation, advance foundation model development that incorporates gene-dosage effects, and accelerate biological discoveries.

Background: Immunotherapies have shown great anti-tumour effect in a variety of malignancies. In multiple myeloma (MM) antibodies, including bispecific T cell engagers, antibody-drug conjugates, and more recently, CAR T cells have reported exciting clinical results and many of them have been incorporated in the treatment armamentarium. Less is reported for NK cells, in particular autologous NK cells. Initial results from our first-in-human trial ACP-001 with autologous NK cells given as consolidation after front-line autologous stem cell transplantation (ASCT) were recently reported (Nahi et al., 2022, Cell Reports Medicine 3, 100508 February 15, 2022). It showed that the concept was feasible with good safety, including no SAEs, and promising efficacy. We here report the long-term clinical follow-up. Aims: The aim of this report was to investigate long-term safety, disease progression, second-line therapy and survival after autologous NK cell treatment. Methods: This first-in-human trial included six patients with newly diagnosed MM eligible for ASCT at the Karolinska University Hospital Huddinge in Sweden. After standard induction treatment (bortezomib, cyclophosphamide and dexamethasone (VCD) at the time) and ASCT with melphalan 200 mg/m2 (MEL200) the patients received three escalating doses of autologous activated and expanded NK cells. Clinical data on long-term safety, disease progression, second-line therapy and survival were captured from the patients’ electronical charts. Results: No subject were lost to follow-up or had withdrawn from the study. With a median follow-up from study inclusion of 6.9 (6.1-7.2) yrs, and 6.2 (5.4-6.7) yrs from the first NK cell infusion, there are no new reported AE related to the NK cell infusions. All six patients are alive with one subject still in first remission 6.8 yrs after inclusion. Five patients had disease progression 13-51 months after study inclusion and four of them underwent reinduction (VRD (n=2), KRD (n=1), KRD+dara (n=1)) followed by a second ASCT with MEL200. The fifth patient progressed within the first yr after ASCT and received VRD+dara. All five patients responded to second line treatment with PR (n=2), VGPR (n=2) and MRD negative (n=1) but subsequently progressed with a PFS2 ranging from 11.5 to 26.3 months. Summary/Conclusion: This long-term follow-up confirms the safety and feasibility of autologous NK cell therapy as consolidation after front line ASCT in MM. Autologous NK cell treatment in first line did not negatively impact the possibility to administer, or the outcome, of later treatments which is important with all new treatment options for patients with advanced MM.

Nuclear hormone receptors are ligand-activated transcription factors that regulate gene expression and play a critical role in endocrine signaling. Orphan nuclear receptors belong to this gene super-family but their target genes and physiological function have not been completely elucidated. In recent years, the identification of natural ligands for these orphan receptors, their expression pattern in different tissues and studies with knock-out animals has delineated distinct regulatory functions for these proteins. The orphans belonging to the PPAR, LXR and FXR family function as lipid and bile-acid sensors while PXR and CAR function as xenobiotic sensors. This review will describe the discovery of natural and synthetic ligands for a number of these orphan receptors (excluding the PPARs) and the identification and characterization of novel signaling pathways and new hormone response systems linked to these targets. Small-molecule modulators of LXR and FXR control key genes involved in cholesterol and lipid metabolism. PXR is a highly promiscuous xenosensor that responds to xenobiotic ligands (antibiotics, statins, glucocorticoids) and induces the Cyp3A gene, thereby playing a role in hepatoprotection and bile acid metabolism. A related receptor from the gene subfamily, CAR, displays high ligand selectivity and modulation of its activity in humans may significantly alter metabolism of drugs and other xenobiotics. The role of the ER relatives, the ERRs will become more apparent as ligands are identified and linked to target genes and physiological function. These targets offer multiple opportunities for therapeutic intervention with small-molecule drugs, in diseases related to neuronal function, inflammation, lipid homeostasis, metabolic function and cancer.

Our laboratory has demonstrated that treatment of MCF-7 breast cancer cells with melatonin (Mlt) followed 24h later with physiological concentrations of all-trans retinoic acid (atRA) results in apoptosis. These studies were extended into trials using the N-nitroso-N-methylurea (NMU)-induced rat mammary tumor model. Initial studies conducted by feeding the animals 9-cis-retinoic acid (9cRA in the chow) and administering melatonin by subcutaneous injection in the late afternoon demonstrated that the combination of Mlt and 9cRA was able to significantly prevent tumor development, and that the combination was more efficacious that either Mlt or 9cRA alone. In this report, we conducted studies to determine if lower doses of 9cRA could be used in combination with Mlt while still maintaining anti-tumor activity and if the route of administration of 9cRA (bolus (gavage) v.s. chronic (chow) routes) affected its interaction with Mlt. The studies presented here demonstrate that significantly reduced doses of 9cRA can be used in combination with Mlt while maintaining anti-tumor efficacy. Furthermore, our studies demonstrate that 9cRA is equally effective when it is administered chronically (chow) or as a bolus (gavage). These data demonstrate that the combined use of Mlt and 9cRA produces additive or synergistic effects, which are more efficacious than 9cRA alone. This combination of Mlt and 9cRA could be a potentially useful clinical treatment regimen for breast cancer since it allows the use of lower doses of retinoic acid, thus, avoiding the toxic side effects associated with the use of high dose retinoids.