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MSTPublications: January 2024

Posted by on Tuesday, January 30, 2024 in New Publications .

Approximating Projections of Conformational Boltzmann Distributions with AlphaFold2 Predictions: Opportunities and Limitations.
Brown BP, Stein RA, Meiler J, Mchaourab HS.
J Chem Theory Comput. 2024 Jan 12. doi: 10.1021/acs.jctc.3c01081. Online ahead of print.

Protein thermodynamics is intimately tied to biological function and can enable processes such as signal transduction, enzyme catalysis, and molecular recognition. The relative free energies of conformations that contribute to these functional equilibria evolved for the physiology of the organism. Despite the importance of these equilibria for understanding biological function and developing treatments for disease, computational and experimental methods capable of quantifying the energetic determinants of these equilibria are limited to systems of modest size. Recently, it has been demonstrated that the artificial intelligence system AlphaFold2 can be manipulated to produce structurally valid protein conformational ensembles. Here, we extend these studies and explore the extent to which AlphaFold2 contact distance distributions can approximate projections of the conformational Boltzmann distributions. For this purpose, we examine the joint probability distributions of inter-residue contact distances along functionally relevant collective variables of several protein systems. Our studies suggest that AlphaFold2 normalized contact distance distributions can correlate with conformation probabilities obtained with other methods but that they suffer from peak broadening. We also find that the AlphaFold2 contact distance distributions can be sensitive to point mutations. Overall, we anticipate that our findings will be valuable as the community seeks to model the thermodynamics of conformational changes in large biomolecular systems.


3D Specimen Scanning and Mapping in Musculoskeletal Oncology: A Feasibility Study.
Colazo JM, Prasad K, Miller A, Sharif K, Aweeda M, Fassler C, Singh R, Schwartz HS, Lawrenz JM, Holt GE, Topf MC.
Ann Surg Oncol. 2023 Dec 22. doi: 10.1245/s10434-023-14757-w. Online ahead of print.

Background: Surgical resection is the primary treatment for bone and soft tissue tumors. Negative margin status is a key factor in prognosis. Given the three-dimensional (3D) anatomic complexity of musculoskeletal tumor specimens, communication of margin results between surgeons and pathologists is challenging. We sought to perform ex vivo 3D scanning of musculoskeletal oncology specimens to enhance communication between surgeons and pathologists.
Methods: Immediately after surgical resection, 3D scanning of the fresh specimen is performed prior to frozen section analysis. During pathologic grossing, whether frozen or permanent, margin sampling sites are annotated on the virtual 3D model using computer-aided design (CAD) software.
Results: 3D scanning was performed in seven cases (six soft tissue, one bone), with specimen mapping on six cases. Intraoperative 3D scanning and mapping was performed in one case in which the location of margin sampling was shown virtually in real-time to the operating surgeon to help achieve a negative margin. In six cases, the 3D model was used to communicate final permanent section analysis. Soft tissue, cartilage, and bone (including lytic lesions within bone) showed acceptable resolution.
Conclusions: Virtual 3D scanning and specimen mapping is feasible and may allow for enhanced documentation and communication. This protocol provides useful information for anatomically complex musculoskeletal tumor specimens. Future studies will evaluate the effect of the protocol on positive margin rates, likelihood that a re-resection contains additional malignancy, and exploration of targeted adjuvant radiation protocols using a patient-specific 3D specimen map.


ent-Verticilide B1 inhibits type 2 ryanodine receptor channels and is antiarrhythmic in Casq2-/- mice.
Gochman A, Do TQ, Kim K, Schwarz JA, Thorpe MP, Blackwell DJ, Ritschel P, Smith AN, Rebbeck RT, Akers WS, Cornea RL, Laver DR, Johnston JN, Knollmann BC.
Mol Pharmacol. 2024 Jan 22:MOLPHARM-AR-2023-000752. doi: 10.1124/molpharm.123.000752. Online ahead of print.

Ca2+ leak from cardiac ryanodine receptor (RyR2) is an established mechanism of sudden cardiac death (SCD), whereby dysregulated Ca2+ handling causes ventricular arrhythmias. We previously discovered the RyR2-selective inhibitor ent-(+)-verticilide (ent-1), a 24-membered cyclooligomeric depsipeptide that is the enantiomeric form of a natural product (nat-(-)-verticilide). Here, we examined its 18-membered ring-size oligomer (ent-verticilide B1; ent-B1) in single RyR2 channel assays, [3H]ryanodine binding assays, and in Casq2-/- cardiomyocytes and mice, a gene-targeted model of SCD. ent-B1 inhibited RyR2 single-channels and [3H]ryanodine binding with low micromolar potency, and RyR2-mediated spontaneous Ca2+ release in Casq2-/- cardiomyocytes with sub-micromolar potency. ent-B1 was a partial RyR2 inhibitor, with maximal inhibitory efficacy of less than 50%. ent-B1 was stable in plasma, with a peak plasma concentration of 1460 ng/ml at 10 min and half-life of 45 min after intraperitoneal administration of 3 mg/kg in mice. Both 3 mg/kg and 30 mg/kg ent-B1 significantly reduced catecholamine-induced ventricular arrhythmia in Casq2-/- mice. Hence, we have identified a novel chemical entity, ent-B1, that preserves the mechanism of action of a hit compound and shows therapeutic efficacy. These findings strengthen RyR2 as an antiarrhythmic drug target and highlight the potential of investigating the mirror-image isomers of natural products to discover new therapeutics. Significance Statement The cardiac ryanodine receptor (RyR2) is an untapped target in the stagnant field of antiarrhythmic drug development. We have confirmed RyR2 as an antiarrhythmic target in a mouse model of sudden cardiac death and shown the therapeutic efficacy of a second enantiomeric natural product.


Longitudinal profiling of the intestinal microbiome in children with cystic fibrosis treated with elexacaftor-tezacaftor-ivacaftor.
Reasoner SA, Bernard R, Waalkes A, Penewit K, Lewis J, Sokolow AG, Brown RF, Edwards KM, Salipante SJ, Hadjifrangiskou M, Nicholson MR.
mBio. 2024 Jan 26:e0193523. doi: 10.1128/mbio.01935-23. Online ahead of print.

The intestinal microbiome influences growth and disease progression in children with cystic fibrosis (CF). Elexacaftor-tezacaftor-ivacaftor (ELX/TEZ/IVA), the newest pharmaceutical modulator for CF, restores the function of the pathogenic mutated CF transmembrane conductance regulator (CFTR) channel. We performed a single-center longitudinal analysis of the effect of ELX/TEZ/IVA on the intestinal microbiome, intestinal inflammation, and clinical parameters in children with CF. Following ELX/TEZ/IVA, children with CF had significant improvements in body mass index and percent predicted forced expiratory volume in one second, and required fewer antibiotics for respiratory infections. Intestinal microbiome diversity increased following ELX/TEZ/IVA coupled with a decrease in the intestinal carriage of Staphylococcus aureus, the predominant respiratory pathogen in children with CF. There was a reduced abundance of microbiome-encoded antibiotic resistance genes. Microbial pathways for aerobic respiration were reduced after ELX/TEZ/IVA. The abundance of microbial acid tolerance genes was reduced, indicating microbial adaptation to increased CFTR function. In all, this study represents the first comprehensive analysis of the intestinal microbiome in children with CF receiving ELX/TEZ/IVA.IMPORTANCECystic fibrosis (CF) is an autosomal recessive disease with significant gastrointestinal symptoms in addition to pulmonary complications. Recently approved treatments for CF, CF transmembrane conductance regulator (CFTR) modulators, are anticipated to substantially improve the care of people with CF and extend their lifespans. Prior work has shown that the intestinal microbiome correlates with health outcomes in CF, particularly in children. Here, we study the intestinal microbiome of children with CF before and after the CFTR modulator, ELX/TEZ/IVA. We identify promising improvements in microbiome diversity, reduced measures of intestinal inflammation, and reduced antibiotic resistance genes. We present specific bacterial taxa and protein groups which change following ELX/TEZ/IVA. These results will inform future mechanistic studies to understand the microbial improvements associated with CFTR modulator treatment. This study demonstrates how the microbiome can change in response to a targeted medication that corrects a genetic disease.


Three-dimensional histology reveals dissociable human hippocampal long axis gradients of Alzheimer’s pathology.
Ortega-Cruz D, Bress KS, Gazula H, Rabano A, Iglesias JE, Strange BA.
bioRxiv. 2023 Dec 7:2023.12.05.570038. doi: 10.1101/2023.12.05.570038. Preprint.

Robust fiber orientation distribution function estimation using deep constrained spherical deconvolution for diffusion-weighted magnetic resonance imaging.
Yao T, Rheault F, Cai LY, Nath V, Asad Z, Newlin N, Cui C, Deng R, Ramadass K, Shafer A, Resnick S, Schilling K, Landman BA, Huo Y.
J Med Imaging (Bellingham). 2024 Jan;11(1):014005. doi: 10.1117/1.JMI.11.1.014005. Epub 2024 Jan 5.

Protein kinase C delta regulates mononuclear phagocytes and hinders response to immunotherapy in cancer.
Chaib M, Holt JR, Fisher EL, Sipe LM, Bohm MS, Joseph SC, Simmons BW, Eugin Simon S, Yarbro JR, Tanveer U, Halle JL, Carson JA, Hollingsworth TJ, Wei Q, Rathmell JC, Thomas PG, Hayes DN, Makowski L.
Sci Adv. 2023 Dec 22;9(51):eadd3231. doi: 10.1126/sciadv.add3231. Epub 2023 Dec 22.

Large Language Models Facilitate the Generation of Electronic Health Record Phenotyping Algorithms.
Yan C, Ong HH, Grabowska ME, Krantz MS, Su WC, Dickson AL, Peterson JF, Feng Q, Roden DM, Stein CM, Kerchberger VE, Malin BA, Wei WQ.
medRxiv. 2023 Dec 19:2023.12.19.23300230. doi: 10.1101/2023.12.19.23300230. Preprint.

Indirect structural changes and reduced controllability after temporal lobe epilepsy resection.
Janson A, Sainburg L, Akbarian B, Johnson GW, Rogers BP, Chang C, Englot DJ, Morgan VL.
Epilepsia. 2024 Jan 19. doi: 10.1111/epi.17889. Online ahead of print.

Piekos JA, Kim J, Keaton JM, Hellwege JN, Edwards TL, Velez Edwards DR.
Pac Symp Biocomput. 2024;29:389-403.

Age-related Muscle Fat Infiltration in Lung Screening Participants: Impact of Smoking Cessation.
Xu K, Li TZ, Terry JG, Krishnan AR, Deppen SA, Huo Y, Maldonado F, Carr JJ, Landman BA, Sandler KL.
medRxiv. 2023 Dec 5:2023.12.05.23299258. doi: 10.1101/2023.12.05.23299258. Preprint.

Multi-site validation of a functional assay to adjudicate SCN5A Brugada Syndrome-associated variants.
Ma JG, O’Neill MJ, Richardson E, Thomson KL, Ingles J, Muhammad A, Solus JF, Davogustto G, Anderson KC, Benjamin Shoemaker M, Stergachis AB, Floyd BJ, Dunn K, Parikh VN, Chubb H, Perrin MJ, Roden DM, Vandenberg JI, Ng CA, Glazer AM.
medRxiv. 2023 Dec 20:2023.12.19.23299592. doi: 10.1101/2023.12.19.23299592. Preprint.

Driver mutation zygosity is a critical factor in predicting clonal hematopoiesis transformation risk.
Kishtagari A, Khan MAW, Li Y, Vlasschaert C, Marneni N, Silver AJ, von Beck K, Spaulding T, Stockton S, Snider C, Sochacki A, Dorand D, Mack TM, Ferrell PB Jr, Xu Y, Bejan CA, Savona MR, Bick AG.
Blood Cancer J. 2024 Jan 15;14(1):6. doi: 10.1038/s41408-023-00974-9.

Repetitive Negative Thinking As a Transdiagnostic Prospective Predictor of Depression and Anxiety Symptoms in Neurodiverse First-Semester College Students.
McKenney EE, Brunwasser SM, Richards JK, Day TC, Kofner B, McDonald RG, Williams ZJ, Gillespie-Lynch K, Kang E, Lerner MD, Gotham KO.
Autism Adulthood. 2023 Dec 1;5(4):374-388. doi: 10.1089/aut.2022.0078. Epub 2023 Dec 12.

ASO Author Reflections: 3D Specimen Scanning in Musculoskeletal Oncology.
Colazo JM, Aweeda M, Fassler C, Singh R, Lawrenz JM, Holt GE, Topf MC.
Ann Surg Oncol. 2024 Jan 3. doi: 10.1245/s10434-023-14848-8. Online ahead of print.

Engineering approaches for RNA-based and cell-based osteoarthritis therapies.
DeJulius CR, Walton BL, Colazo JM, d’Arcy R, Francini N, Brunger JM, Duvall CL.
Nat Rev Rheumatol. 2024 Jan 22. doi: 10.1038/s41584-023-01067-4. Online ahead of print.