Skip to main content

MSTPublications: September 2024

Posted by on Friday, September 27, 2024 in New Publications .

Pharmacologic Hedgehog inhibition modulates the cytokine profile of osteolytic breast cancer cells.
Bennett NE, Parker DV, Mangano RS, Baum JE, Northcutt LA, Miller JS, Beadle EP, Rhoades JA.
J Bone Oncol. 2024 Jul 28;47:100625. doi: 10.1016/j.jbo.2024.100625. eCollection 2024 Aug.

The establishment and progression of bone metastatic breast cancer is supported by immunosuppressive myeloid populations that enable tumor growth by dampening the innate and adaptive immune response. Much work remains to understand how to target these tumor-myeloid interactions to improve treatment outcomes. Noncanonical Hedgehog signaling is an essential component of bone metastatic tumor progression, and prior literature suggests a potential role for Hedgehog signaling and its downstream effector Gli2 in modulating immune responses. In this work, we sought to identify if inhibition of noncanonical Hedgehog signaling alters the cytokine profile of osteolytic breast cancer cells and the subsequent communication between the tumor cells and myeloid cells. Examination of large patient databases revealed significant relationships between Gli2 expression and expression of markers of myeloid maturation and activation as well as cytokine expression. We found that treatment with HPI-1 reduced tumor cell expression of numerous cytokine genes, including CSF1, CSF2, and CSF3, as well as CCL2 and IL6. Secreted CSF-1 (M-CSF) was also reduced by treatment. Changes in tumor-secreted factors resulted in polarization of THP-1 monocytes toward a proinflammatory phenotype, characterized by increased CD14 and CD40 surface marker expression. We therefore propose M-CSF as a novel target of Hedgehog inhibition with potential future applications in altering the immune microenvironment in addition to its known roles in reducing tumor-induced bone disease.

 

Challenges of Imaging the Greater Occipital Nerve Using Magnetic Resonance Imaging.
Reddy A, Saad M, Kassis S, Assi P, Thayer WP, Esteve IVM.
Ann Plast Surg. 2024 Sep 1;93(3S Suppl 2):S130-S131. doi: 10.1097/SAP.0000000000004086.

Migraine headaches are a significant global health concern, frequently managed with varying levels of success. Compression of the greater occipital nerve (GON) is hypothesized to contribute to pathology in some migraine patients, making extracranial nerve decompression surgery a potential intervention for refractory cases. However, accurate methods to image the GON along its tortuous course still need to be explored. Our group has developed magnetic resonance imaging sequences to track the GON. Yet, many challenges were met, which included navigating the GON’s complex anatomy, understanding anatomical variants, and designing advanced magnetic resonance imaging sequences and coils to image the posterior scalp. Addressing these hurdles is vital to capture and understand GON pathology and guide potential interventions.

 

Assays of Variant Effect and Automated Patch Clamping Improve KCNH2-LQTS Variant Classification and Cardiac Event Risk Stratification.
O’Neill MJ, Ng CA, Aizawa T, Sala L, Bains S, Winbo A, Ullah R, Shen Q, Tan CY, Kozek K, Vanags LR, Mitchell DW, Shen A, Wada Y, Kashiwa A, Crotti L, Dagradi F, Musu G, Spazzolini C, Neves R, Bos JM, Giudicessi JR, Bledsoe X, Gamazon ER, Lancaster MC, Glazer AM, Knollmann BC, Roden DM, Weile J, Roth F, Salem JE, Earle N, Stiles R, Agee T, Johnson CN, Horie M, Skinner J, Ackerman MJ, Schwartz PJ, Ohno S, Vandenberg JI, Kroncke BM.
Circulation. 2024 Sep 24. doi: 10.1161/CIRCULATIONAHA.124.069828. Online ahead of print.

Background: Long QT syndrome is a lethal arrhythmia syndrome, frequently caused by rare loss-of-function variants in the potassium channel encoded by KCNH2. Variant classification is difficult, often because of lack of functional data. Moreover, variant-based risk stratification is also complicated by heterogenous clinical data and incomplete penetrance. Here we sought to test whether variant-specific information, primarily from high-throughput functional assays, could improve both classification and cardiac event risk stratification in a large, harmonized cohort of KCNH2 missense variant heterozygotes.
Methods: We quantified cell-surface trafficking of 18 796 variants in KCNH2 using a multiplexed assay of variant effect (MAVE). We recorded KCNH2 current density for 533 variants by automated patch clamping. We calibrated the strength of evidence of MAVE data according to ClinGen guidelines. We deeply phenotyped 1458 patients with KCNH2 missense variants, including QTc, cardiac event history, and mortality. We correlated variant functional data and Bayesian long QT syndrome penetrance estimates with cohort phenotypes and assessed hazard ratios for cardiac events.
Results: Variant MAVE trafficking scores and automated patch clamping peak tail currents were highly correlated (Spearman rank-order ρ=0.69; n=433). The MAVE data were found to provide up to pathogenic very strong evidence for severe loss-of-function variants. In the cohort, both functional assays and Bayesian long QT syndrome penetrance estimates were significantly predictive of cardiac events when independently modeled with patient sex and adjusted QT interval (QTc); however, MAVE data became nonsignificant when peak tail current and penetrance estimates were also available. The area under the receiver operator characteristic curve for 20-year event outcomes based on patient-specific sex and QTc (area under the curve, 0.80 [0.76-0.83]) was improved with prospectively available penetrance scores conditioned on MAVE (area under the curve, 0.86 [0.83-0.89]) or attainable automated patch clamping peak tail current data (area under the curve, 0.84 [0.81-0.88]).
Conclusions: High-throughput KCNH2 variant MAVE data meaningfully contribute to variant classification at scale, whereas long QT syndrome penetrance estimates and automated patch clamping peak tail current measurements meaningfully contribute to risk stratification of cardiac events in patients with heterozygous KCNH2 missense variants.

 

ParSE-seq: a calibrated multiplexed assay to facilitate the clinical classification of putative splice-altering variants.
O’Neill MJ, Yang T, Laudeman J, Calandranis ME, Harvey ML, Solus JF, Roden DM, Glazer AM.
Nat Commun. 2024 Sep 27;15(1):8320. doi: 10.1038/s41467-024-52474-4.

Interpreting the clinical significance of putative splice-altering variants outside canonical splice sites remains difficult without time-intensive experimental studies. To address this, we introduce Parallel Splice Effect Sequencing (ParSE-seq), a multiplexed assay to quantify variant effects on RNA splicing. We first apply this technique to study hundreds of variants in the arrhythmia-associated gene SCN5A. Variants are studied in ‘minigene’ plasmids with molecular barcodes to allow pooled variant effect quantification. We perform experiments in two cell types, including disease-relevant induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs). The assay strongly separates known control variants from ClinVar, enabling quantitative calibration of the ParSE-seq assay. Using these evidence strengths and experimental data, we reclassify 29 of 34 variants with conflicting interpretations and 11 of 42 variants of uncertain significance. In addition to intronic variants, we show that many synonymous and missense variants disrupted RNA splicing. Two splice-altering variants in the assay also disrupt splicing and sodium current when introduced into iPSC-CMs by CRISPR-Cas9 editing. ParSE-seq provides high-throughput experimental data for RNA-splicing to support precision medicine efforts and can be readily adopted to study other loss-of-function genotype-phenotype relationships.

 

Integration of estimated regional gene expression with neuroimaging and clinical phenotypes at biobank scale.
Hoang N, Sardaripour N, Ramey GD, Schilling K, Liao E, Chen Y, Park JH, Bledsoe X, Landman BA, Gamazon ER, Benton ML, Capra JA, Rubinov M.
PLoS Biol. 2024 Sep 13;22(9):e3002782. doi: 10.1371/journal.pbio.3002782. eCollection 2024 Sep.

Subset-specific mitochondrial stress and DNA damage shape T cell responses to fever and inflammation.
Heintzman DR, Sinard RC, Fisher EL, Ye X, Patterson AR, Elasy JH, Voss K, Chi C, Sugiura A, Rodriguez-Garcia GJ, Chowdhury NU, Arner EN, Krystoviak ES, Mason FM, Toudji YT, Steiner KK, Khan W, Olson LM, Jones AL, Hong HS, Bass L, Beier KL, Deng W, Lyssiotis CA, Newcomb DC, Bick AG, Rathmell WK, Wilson JT, Rathmell JC.
Sci Immunol. 2024 Sep 20;9(99):eadp3475. doi: 10.1126/sciimmunol.adp3475. Epub 2024 Sep 20.

Association Between Postsurgical Functional Connectivity and Seizure Outcome in Patients With Temporal Lobe Epilepsy.
Akbarian B, Sainburg LE, Janson A, Johnson G, Doss DJ, Rogers BP, Englot DJ, Morgan VL.
Neurology. 2024 Oct 8;103(7):e209816. doi: 10.1212/WNL.0000000000209816. Epub 2024 Sep 3.

Learning site-invariant features of connectomes to harmonize complex network measures.
Newlin NR, Kanakaraj P, Li T, Pechman K, Archer D, Jefferson A; BIOCARD Study Team; Landman B, Moyer D.
Proc SPIE Int Soc Opt Eng. 2024 Feb;12930:129302E. doi: 10.1117/12.3009645. Epub 2024 Apr 2.

Inter-vendor harmonization of CT reconstruction kernels using unpaired image translation.
Krishnan AR, Xu K, Li T, Gao C, Remedios LW, Kanakaraj P, Lee HH, Bao S, Sandler KL, Maldonado F, Išgum I, Landman BA.
Proc SPIE Int Soc Opt Eng. 2024 Feb;12926:129261D. doi: 10.1117/12.3006608. Epub 2024 Apr 2.

Nucleus subtype classification using inter-modality learning.
Remedios LW, Bao S, Remedios SW, Lee HH, Cai LY, Li T, Deng R, Cui C, Li J, Liu Q, Lau KS, Roland JT, Washington MK, Coburn LA, Wilson KT, Huo Y, Landman BA.
Proc SPIE Int Soc Opt Eng. 2024 Feb;12933:129330F. doi: 10.1117/12.3006237. Epub 2024 Apr 3.

Characterization of Porcine Immunoglobulin Deposition in Human Livers Recovered Using a Xenogeneic Cross-Circulation.
Shishido Y, Tracy KM, Wu WK, Cortelli M, Petrovic M, Harris TR, Simon V, Francois S, Tucker WD, Petree BS, Cardwell NL, Ukita R, Demarest CT, Alexopoulos SP, Shaver CM, Bacchetta M.
ASAIO J. 2024 Sep 18. doi: 10.1097/MAT.0000000000002311. Online ahead of print.

The Departmental Scholarly Index: A Metric of Research Productivity.
James AJ, Popa N, Reddy AP, Torres-Guzman RA, Perdikis G, Lineaweaver WC.
Ann Plast Surg. 2024 Sep 1;93(3S Suppl 2):S127-S129. doi: 10.1097/SAP.0000000000004083.

Diffusion Tensor Imaging: Techniques and Applications for Peripheral Nerve Injury.
Chaker SC, Reddy AP, King D, Manzanera Esteve IV, Thayer WP.
Ann Plast Surg. 2024 Sep 1;93(3S Suppl 2):S113-S115. doi: 10.1097/SAP.0000000000004055.

Multiancestry transferability of a polygenic risk score for diverticulitis.
Ueland TE, Mosley JD, Neylan C, Shelley JP, Robinson J, Gamazon ER, Maguire L, Peek R, Hawkins AT.
BMJ Open Gastroenterol. 2024 Sep 23;11(1):e001474. doi: 10.1136/bmjgast-2024-001474.

Longitudinal Symptom Burden and Pharmacologic Management of Catatonia in Autism with and without Profound Impairment: An Observational Study.
Smith JR, Lim S, Bindra S, Marler S, Rajah B, Williams ZJ, Baldwin I, Hossain N, Wilson JE, Fuchs DC, Luccarelli J.
medRxiv [Preprint]. 2024 Sep 6:2024.09.05.24312724. doi: 10.1101/2024.09.05.24312724.