Multiscale profiling of enzyme activity in cancer

Diverse processes in cancer are mediated by enzymes, which most proximally exert their function through their activity. Methods to quantify enzyme activity, rather than just expression, are therefore critical to our ability to understand the pathological roles of enzymes in cancer and to harness this class of biomolecules as diagnostic and therapeutic targets. Here we present an integrated set of methods for measuring specific enzyme activities across the organism, tissue, and cellular levels, which we unify into a methodological hierarchy to facilitate biological discovery. We focus on proteases for method development and validate our approach through the study of tumor progression and treatment response in an autochthonous model of Alk-mutant lung cancer. To quantitatively measure activity dynamics over time, we engineered multiplexed, peptide-based nanosensors to query protease activity in vivo. Machine learning analysis of sensor measurements revealed dramatic protease dysregulatio..... READ ARTICLE

BioRxiv DOI:10.1101/2021.11.11.468288

Authors: Ava P. Soleimany, Jesse D. Kirkpatrick, Cathy S. Wang, Alex M. Jaeger, Susan Su, Santiago Naranjo, Qian Zhong, Christina M. Cabana, Tyler Jacks, Sangeeta N. Bhatia

Review Paper, group2Kirk SmithNovember 12, 2021Multiscale profiling, enzyme activity, cancer

Structural basis of cytokine-mediated activation of ALK family receptors

Anaplastic lymphoma kinase (ALK)1 and the related leukocyte tyrosine kinase (LTK)2 are recently deorphanized receptor tyrosine kinases3. Together with their activating cytokines, ALKAL1 and ALKAL24,5,6 (also called FAM150A and FAM150B or AUGβ and AUGα, respectively), they are involved in neural development7, cancer7,8,9 and autoimmune diseases10. Furthermore, mammalian ALK recently emerged as a key regulator of energy expenditure and weight gain11, consistent with a metabolic role for Drosophila ALK12. Despite such functional pleiotropy and growing therapeutic relevance13,14, structural insights into ALK and LTK and their complexes with cognate cytokines have remained scarce. Here we show that the cytokine-binding segments of human ALK and LTK comprise a novel architectural chimera of a permuted TNF-like module that braces a glycine-rich subdomain featuring a hexagonal lattice of long polyglycine type II helices. The cognate cytokines ALKAL1 and ALKAL2 are monomeric three-helix bundles..... READ ARTICLE

Nature DOI:10.1038/s41586-021-03959-5

Authors: Steven De Munck, Mathias Provost, Michiko Kurikawa, Ikuko Omori, Junko Mukohyama, Jan Felix, Yehudi Bloch, Omar Abdel-Wahab, J. Fernando Bazan, Akihide Yoshimi & Savvas N. Savvides

Pre-Clinical, group2Kirk SmithOctober 13, 2021cancer, metabolism, X-ray crystallography, ALK

Prevalence and potential biological role ofTERTamplifications inALKtranslocated adenocarcinoma of the lung

The advent of specific ALK-targeting drugshas radically changed the outcome of patients withALKtranslocated non-small-cell lung cancer(NSCLC). However, emerging resistance to treatmentwithALKinhibitors in these patients remains amajor concern. In previous studies, we analysed twoALK+patient cohorts (TP53wild-type/TP53mutated) in terms of copy number alterations. Allpatients belonging to theTP53wild-type group hadmainly genetically stable genomes, with one excep-tion showing chromosomal instability and amplifica-tions of several gene loci, includingTERT. Here, weaimed to determine the prevalence ofTERTamplifi-cations in theseALK+lung cancer patients by ana-lysing an independent cohort of 109ALKtranslocated cases. We further analysed the copy numbers of numerous cancer-relevant genes andother genetic aberrations. The prevalence ofTERTamplifi-cations was determined by means of FISH analyses.Copy numbers of 87 cancer-relevant genes were deter-mined by NanoString nCounterâtechnolo..... READ ARTICLE

Histopathology DOI:10.1111/his.14256

Authors: Alidousty C, Duerbaum N, Wagener-Ryczek S, Baar T, Martelotto L G, Heydt C, Siemanowski J, Holz B, Binot E,Fassunke J, Merkelbach-Bruse S, Wolf J, Kron A, Buettner R, Schultheis A M

Pre-ClinicalKirk SmithSeptember 18, 2020ALK, cancer, lung, TERT, genetic stability

Inhibition of MEK alone and in combination with ALK inhibition suppresses tumor growth in a mouse model of ALK positive lung cancer

Anaplastic lymphoma kinase (ALK)-positive non-small cell lung cancer most commonly arises through EML4-ALK chromosomal fusion. We have previously demonstrated that combination of the ALK inhibitor crizotinib with the MEK inhibitor selumetinib was highly effective at reducing cell viability of ALK-positive NSCLC (H3122) cells. In this study, we further investigated the efficacy of crizotinib and selumetinib combination therapy in an in vivo xenograft model of ALK-positive lung cancer. Crizotinib decreased tumor volume by 52% compared to control, and the drug combination reduced tumor growth compared to crizotinib. In addition, MEK inhibition alone reduced tumor growth by 59% compared to control. Crizotinib, selumetinib, alone and in combination were non-toxic at the dose of 25 mg/kg with values for ALT (< 80 U/L) and creatinine (<2 mg/dL) within the normal range. Our results support the combined use of crizotinib with selumetinib in ALK-positive lung cancer but raise the possibility tha..... READ ARTICLE

Journal of Pharmacology and Experimental Therapeutics DOI:10.1124/jpet.120.266049

Authors: Nensi Shrestha, Abigail R Bland, Rebecca L Bower, Rhonda Rosengren, John Ashton

Pre-ClinicalKirk SmithApril 13, 2020ALK, MEK, Crizotinib, cancer, chemotherapy, receptor tyrosine kinases (RTKs)

Tyrosine phosphorylation is critical for ACLY activity in lipid metabolism and cancer

A fundamental requirement for growth of rapidly proliferating cells is metabolic adaptation to promote synthesis of biomass1. ATP citrate lyase (ACLY) is a critical enzyme responsible for synthesis of cytosolic acetyl-CoA, the key building component for de novo fatty acid synthesis and links vital pathways such as carbohydrate and lipid metabolism2. The mechanisms of ACLY regulation are not completely understood and the regulation of ACLY function by tyrosine phosphorylation is unknown... Our results reveal a novel mechanism for direct ACLY regulation that is subverted by multiple oncogenically-activated tyrosine kinases in diverse human cancers. These findings have significant implications for novel therapies targeting ACLY in cancer and metabolism. READ ARTICLE

BioRxiv DOI:10.1101/2020.01.20.910752

Authors: Johnvesly Basappa, Mahmoud A. ElAzzouny, Delphine C.M. Rolland, Anagh A. Sahasrabuddhe, Kaiyu Ma, Gleb A. Bazilevsky, Steven R. Hwang, Venkatesha Basrur, Kevin P. Conlon, Nathanael G. Bailey, John K. Frederiksen, Santiago Schnell, Yeqiao Zhou, David Cookmeyer, Jan M. Pawlicki, Amit Dipak Amin, James L. Riley, Robert B. Faryabi, Jonathan H Schatz, Kathryn E. Wellen, Ronen Marmorstein, Charles F. Burant, Kojo S.J. Elenitoba-Johnson, Megan S. Lim