Dana-Farber's Research News - July 15, 2021

Read more about the highlights the research endeavors at Dana-Farber Cancer Institute, noting recently published papers available from PubMed where Dana-Farber faculty are listed as first or senior authors. 

July 15, 2021

Blood

BH3 Profiling Identifies Ruxolitinib as a Promising Partner for Venetoclax to Treat T-Cell Prolymphocytic Leukemia

Herbaux C, Chong SJF, Collins MC, Valentin R, Hackett L, Ng S, Davids MS

Conventional therapies for patients with T-cell prolymphocytic leukemia (T-PLL), such as cytotoxic chemotherapy and alemtuzumab, have limited efficacy and considerable toxicity. Several novel agent classes have demonstrated preclinical activity in T-PLL, including inhibitors of the JAK/STAT and T-cell receptor pathways, as well as histone deacetylase (HDAC) inhibitors. Recently, the BCL-2 inhibitor venetoclax also showed some clinical activity in T-PLL. We sought to characterize functional apoptotic dependencies in T-PLL to identify a novel combination therapy in this disease. Twenty-four samples from patients with primary T-PLL were studied by using BH3 profiling, a functional assay to assess the propensity of a cell to undergo apoptosis (priming) and the relative dependence of a cell on different antiapoptotic proteins. Primary T-PLL cells had a relatively low level of priming for apoptosis and predominantly depended on BCL-2 and MCL-1 proteins for survival. Selective pharmacologic inhibition of BCL-2 or MCL-1 induced cell death in primary T-PLL cells. Targeting the JAK/STAT pathway with the JAK1/2 inhibitor ruxolitinib or HDAC with belinostat both independently increased dependence on BCL-2 but not MCL-1, thereby sensitizing T-PLL cells to venetoclax. Based on these results, we treated 2 patients with refractory T-PLL with a combination of venetoclax and ruxolitinib. We observed a deep response in JAK3-mutated T-PLL and a stabilization of the nonmutated disease. Our functional, precision-medicine-based approach identified inhibitors of HDAC and the JAK/STAT pathway as promising combination partners for venetoclax, warranting a clinical exploration of such combinations in T-PLL.


Blood

The HCK/BTK Inhibitor KIN-8194 is Active in MYD88 Driven Lymphomas and Overcomes Mutated BTKCys481 Ibrutinib Resistance

Yang G, Wang J, Tan L, Munshi M, Liu X, Kofides A, Chen JG, Tsakmaklis N, Demos M, Guerrera ML, Xu L, Hunter ZR, Che J, Patterson CJ, Meid KE, Castillo J, Munshi NC, Anderson KC, Buhrlage S, Gray NSS, Treon SPP

Activating mutations in MYD88 promote malignant cell growth and survival through HCK mediated BTK activation. Ibrutinib binds to BTKCys481 and is active in B-cell malignancies driven by mutated MYD88. Mutations in BTKCys481 particularly BTKCys481Ser are common in patients with acquired ibrutinib resistance. We therefore performed an extensive medicinal chemistry campaign and identified KIN-8194 as a novel dual inhibitor of HCK and BTK. KIN-8194 showed potent and selective in vitro killing of MYD88 mutated lymphoma cells, including ibrutinib resistant BTKCys481Ser expressing cells. KIN-8194 demonstrated excellent bioavailability and pharmacokinetic parameters, with good tolerance in rodent models at pharmacologically achievable and active doses. Pharmacodynamic studies

showed sustained HCK and BTK inhibition for 24 hours following single oral administration of KIN-8194 in MYD88 mutated TMD-8 ABC DLBCL xenografted mice with either wild-type BTK (BTKWT) or BTKCys481Ser expressing tumors. KIN-8194 showed superior survival benefit over ibrutinib in both BTKWT and BTKCys481Ser expressing TMD-8 DLBCL xenografted mice, including sustained complete responses >12 weeks off treatment in mice with BTKWT expressing TMD-8 tumors. The Bcl-2 inhibitor venetoclax enhanced the anti-tumor activity of KIN-8194 in BTKWT and BTKCys481Ser expressing MYD88 mutated lymphoma cells, and markedly reduced tumor growth and prolonged survival in mice with BTKCys481Ser expressing TMD-8 tumors treated with both drugs. The findings highlight the feasibility of targeting HCK, a key driver of mutated MYD88 pro-survival signaling, and provide a framework for the advancement of KIN-8194 for human studies in B-cell malignancies driven by HCK and BTK.


Cancer Discovery

Discovery and Features of an Alkylating Signature in Colorectal Cancer

Gurjao C, Zhong R, Haruki K, Li YY, Spurr LF, Reardon B, Ugai T, Zhang X, Cherniack AD, Song M, Van Allen EM, Meyerhardt JA, Nowak JA, Giovannucci EL, Wu K, Ogino S, Giannakis M

Several risk factors have been established for colorectal carcinoma (CRC), yet their direct mutagenic effects in patients' tumours remain to be elucidated. Here, we leveraged whole-exome sequencing data from 900 CRC cases that had occurred in three US-wide prospective studies with extensive dietary and lifestyle information. We found an alkylating signature which was previously undescribed in CRC, and then showed the existence of a similar mutational process in normal colonic crypts. This alkylating signature is associated with high intakes of processed and unprocessed red meat prior to diagnosis. Additionally, this signature was more abundant in the distal colorectum, predicted to target cancer driver mutations KRAS p.G12D, KRAS p.G13D and PIK3CA p.E5454K, and associated with poor survival. Together, these results link for the first time a colorectal mutational signature to a component of diet, and further implicate the role of red meat in CRC initiation and progression.


Molecular Cell

TIRR Inhibits the 53BP1-p53 Complex to Alter Cell-Fate Programs

Parnandi N, Rendo V, Nguyen H, Drane P, Beroukhim R, Chowdhury D

53BP1 influences genome stability via two independent mechanisms: (1) regulating DNA double-strand break (DSB) repair and (2) enhancing p53 activity. We discovered a protein, Tudor-interacting repair regulator (TIRR), that associates with the 53BP1 Tudor domain and prevents its recruitment to DSBs. Here, we elucidate how TIRR affects 53BP1 function beyond its recruitment to DSBs and biochemically links the two distinct roles of 53BP1. Loss of TIRR causes an aberrant increase in the gene transactivation function of p53, affecting several p53-mediated cell-fate programs. TIRR inhibits the complex formation between the Tudor domain of 53BP1 and a dimethylated form of p53 (K382me2) that is poised for transcriptional activation of its target genes. TIRR mRNA expression levels negatively correlate with the expression of key p53 target genes in breast and prostate cancers. Further, TIRR loss is selectively not tolerated in p53-proficient tumors. Therefore, we establish that TIRR is an important inhibitor of the 53BP1-p53 complex.


New England Journal of Medicine

Idecabtagene Vicleucel in Relapsed Myeloma Reply

Munshi NC

To the Editor: Munshi et al. (Feb. 25 issue) report that treatment with idecabtagene vicleucel (ide-cel) led to responses in heavily pretreated patients with relapsed and refractory myeloma. Ide-cel recognizes B-cell maturation antigen (BCMA), which is dominantly expressed on the surface of mature B lymphocytes. The soluble BCMA (sBCMA) level is a promising biomarker for predicting outcomes in patients with multiple myeloma and was investigated longitudinally in this trial.


New England Journal of Medicine

Acquired Resistance to KRAS(G12C) Inhibition in Cancer

Awad MM, Liu S, Dilly J, Heist RS, Jacobson JO, Yang X, Persky NS, Root DE, Lowder KE, Feng H, Haigis KM, Hung YP, Sholl LM, Wolpin BM, Jänne PA, Aguirre AJ

BACKGROUND: Clinical trials of the KRAS inhibitors adagrasib and sotorasib have shown promising activity in cancers harboring KRAS glycine-to-cysteine amino acid substitutions at codon 12 (KRASG12C). The mechanisms of acquired resistance to these therapies are currently unknown.

METHODS: Among patients with KRASG12C -mutant cancers treated with adagrasib monotherapy, we performed genomic and histologic analyses that compared pretreatment samples with those obtained after the development of resistance. Cell-based experiments were conducted to study mutations that confer resistance to KRASG12C inhibitors.

RESULTS: A total of 38 patients were included in this study: 27 with

non-small-cell lung cancer, 10 with colorectal cancer, and 1 with appendiceal cancer. Putative mechanisms of resistance to adagrasib were detected in 17 patients (45% of the cohort), of whom 7 (18% of the cohort) had multiple coincident mechanisms. Acquired KRAS alterations included G12D/R/V/W, G13D, Q61H, R68S, H95D/Q/R, Y96C, and high-level amplification of the KRASG12C allele. Acquired bypass mechanisms of resistance included MET amplification; activating mutations in NRAS, BRAF, MAP2K1, and RET; oncogenic fusions involving ALK, RET, BRAF, RAF1, and FGFR3; and loss-of-function mutations in NF1 and PTEN. In two of nine patients with lung adenocarcinoma for whom paired tissue-biopsy samples were available, histologic transformation to squamous-cell carcinoma was observed without identification of any other resistance mechanisms. Using an in vitro deep mutational scanning screen, we systematically defined the landscape of KRAS mutations that confer resistance to KRASG12C inhibitors.

CONCLUSIONS: Diverse genomic and histologic mechanisms impart resistance to covalent KRASG12C inhibitors, and new therapeutic strategies are required to delay and overcome this drug resistance in patients with cancer. (Funded by Mirati Therapeutics and others; ClinicalTrials.gov number, NCT03785249.).


Nature Communications

Identification of Optimal Dosing Schedules of Dacomitinib and Osimertinib for a Phase I/II Trial in Advanced EGFR-Mutant Non-Small Cell Lung Cancer

Poels KE, Frisco-Cabanos H, Chakrabarti S, Napoli C, McDonald TO, Hata A, Michor F

Despite the clinical success of the third-generation EGFR inhibitor osimertinib as a first-line treatment of EGFR-mutant non-small cell lung cancer (NSCLC), resistance arises due to the acquisition of EGFR second-site mutations and other mechanisms, which necessitates alternative therapies. Dacomitinib, a pan-HER inhibitor, is approved for first-line treatment and results in different acquired EGFR mutations than osimertinib that mediate on-target resistance. A combination of osimertinib and dacomitinib could therefore induce more durable responses by preventing the emergence of resistance. Here we present an integrated computational modeling and experimental approach to identify an optimal dosing schedule for osimertinib and dacomitinib combination therapy. We developed a predictive model that encompasses tumor heterogeneity and inter-subject pharmacokinetic variability to predict tumor evolution under different dosing schedules, parameterized using in vitro dose-response data. This model was validated using cell line data and used to identify an optimal combination dosing schedule. Our schedule was subsequently confirmed tolerable in an ongoing dose-escalation phase I clinical trial (NCT03810807), with some dose modifications, demonstrating that our rational modeling approach can be used to identify appropriate dosing for combination therapy in the clinical setting.


Proceedings of the National Academy of Science of the U.S.A.

Molecular Design of the gdT Cell Receptor Ectodomain Encodes Biologically Fit Ligand Recognition in the Absence of Mechanosensing

Mallis RJ, Duke-Cohan JS, Akitsu A, Tetteh PW, Hussey RE, Lawney B, Brazin KN, Reinherz EL

High-acuity abT cell receptor (TCR) recognition of peptides bound to major histocompatibility complex molecules (pMHCs) requires mechanosensing, a process whereby piconewton (pN) bioforces exert physical load on abTCR-pMHC bonds to dynamically alter their lifetimes and foster digital sensitivity cellular signaling. While mechanotransduction is operative for both abTCRs and pre-TCRs within the abT lineage, its role in gdT cells is unknown. Here, we show that the human DP10.7 gdTCR specific for the sulfoglycolipid sulfatide bound to CD1d only sustains a significant load and undergoes force-induced structural transitions when the binding interface-distal gd constant domain (C) module is replaced with that of ab. The chimeric gd-abTCR also signals more robustly than does the wild-type (WT) gdTCR, as revealed by RNA-sequencing (RNA-seq) analysis of TCR-transduced Rag2 -/- thymocytes, consistent with structural, single-molecule, and molecular dynamics studies reflective of gdTCRs as mediating recognition via a more canonical immunoglobulin-like receptor interaction. Absence of robust, force-related catch bonds, as well as gdTCR structural transitions, implies that gdT cells do not use mechanosensing for ligand recognition. This distinction is consonant with the fact that their innate-type ligands, including markers of cellular stress, are expressed at a high copy number relative to the sparse pMHC ligands of abT cells arrayed on activating target cells. We posit that mechanosensing emerged over ~200 million years of vertebrate evolution to fulfill indispensable adaptive immune recognition requirements for pMHC in the abT cell lineage that are unnecessary for the gdT cell lineage mechanism of non-pMHC ligand detection.


American Journal of Clinical Oncology

Dermal Lymphatic Invasion, Survival, and Time to Recurrence or Progression in Inflammatory Breast Cancer

Remolano MC, Schlossman J, Harrison B, Yeh E, Jacene H, Nakhlis F, Block C, Rosenbluth JM, Garrido-Castro AC, Overmoyer BA


Annals of Nuclear Medicine

Correlation of 68Ga-DOTATATE Uptake on PET/CT with Pathologic Features of Cellular Proliferation in Neuroendocrine Neoplasms

Karls S, Kravets S, Wang Y, Cheng S, Perez K, Chan J, Jacene H


Biometrics

Integration of Survival Data from Multiple Studies

Ventz S, Trippa L


Cancer Letters

The Treatment Landscape of Metastatic Prostate Cancer

Yamada Y, Beltran H


Chemical Society Reviews

Chemoproteomic Methods for Covalent Drug Discovery

Chan WC, Sharifzadeh S, Buhrlage SJ, Marto JA


Database

KMDATA: A Curated Database of Reconstructed Individual Patient-Level Data from 153 Oncology Clinical Trials

Fell G, Redd RA, Rahman R, Arfe A, Alexander BM, Ventz S, Trippa L


Expert Opinion on Investigational Drugs

Advances in the Treatment of Platinum Resistant Epithelial Ovarian Cancer: An Update on Standard and Experimental Therapies

Leung SOA, Konstantinopoulos PA


Expert Review of Anticancer Therapy

The Evolution of Cyclin Dependent Kinase Inhibitors in the Treatment of Cancer

Shapiro GI


Gynecologic Oncology

The American Society of Clinical Oncology 2021 Annual (virtual) Meeting: A Review and Summary of Selected Abstracts

Liu JF


Haematologica

Natural History of Waldenström Macroglobulinemia Following Acquired Resistance to Ibrutinib Monotherapy

Gustine JN, Sarosiek S, Flynn CA, Meid K, Leventoff C, White T, Guerrera ML, Xu L, Kofides A, Tsakmaklis N, Munshi M, Demos M, Patterson CJ, Liu X, Yang G, Hunter ZR, Branagan AR, Treon SP, Castillo JJ


International Journal of Radiation Oncology, Biology, Physics

Practice Consolidation Among U.S. Radiation Oncologists Over Time

Milligan M, Kim DW, John Orav E, Figueroa JF, Lam MB


Journal of Immunotherapy

Myeloid Cell Infiltration Correlates with Prognosis in Cholangiocarcinoma and Varies Based on Tumor Location

Rahma OE


Journal of Sexual Medicine

Culture and Sexual Medicine: A Road Map for Clinical Inquiry and Practice

Bober SL, Chevalier LL


Leukemia and Lymphoma

Anaplastic Lymphoma Kinase-Positive Large B-Cell Lymphoma (ALK+LBCL): A Systematic Review of Clinicopathological Features and Management

Castillo JJ 


Molecular Biology and Evolution

Higher Rates of Processed Pseudogene Acquisition in Humans and Three Great Apes Revealed by Long-Read Assemblies

Feng X, Li H


Neuro-Oncology

The 2021 WHO Classification of Tumors of the Central Nervous System: Clinical Implications

Wen PY 


Nucleic Acids Research

Rigrag: High-Resolution Mapping of Genic Targeting Preferences During HIV-1 Integration In Vitro and In-Vivo

Bedwell GJ, Jang S, Li W, Singh PK, Engelman AN


Pediatric Blood and Cancer

PediCARE: Development of a Poverty-Targeted Intervention for Pediatric Cancer

Umaretiya PJ, Revette A, Seo A, Flamand Y, Ilcisin L, Zheng DJ, Wolfe J, Bona K


PLoS One

Deep Learning to Predict Long-Term Mortality in Patients Requiring 7 Days of Mechanical Ventilation

George N, Moseley E, Siu J, Samuel M, Yam J, Huang K, Celi LA, Lindvall C


Radiotherapy and Oncology

Second Malignancy Probabilities in Prostate Cancer Patients Treated with SBRT and Other Contemporary Radiation Techniques

Dee EC, Muralidhar V, King MT, Martin NE, D'Amico AV, Mouw KW, Orio PF, Nguyen PL, Leeman JE


STAR Protocols

Employing Nanobodies for Immune Landscape Profiling by PET Imaging in Mice

Abousaway OB, Rashidian M


Trends in Cell Biology

REV7 Directs DNA Repair Pathway Choice

Clairmont CS, D'Andrea AD