Geographic differences in lung cancer: focus on carcinogens, genetic predisposition, and molecular epidemiology

Lung cancer poses a global health challenge and stands as the leading cause of cancer-related deaths worldwide. However, its incidence, mortality, and characteristics are not uniform across all regions worldwide. Understanding the factors contributing to this diversity is crucial in a prevalent disease where most cases are diagnosed in advanced stages. Hence, prevention and early diagnosis emerge as the most efficient strategies to enhance outcomes. In Western societies, tobacco consumption constitutes the primary risk factor for lung cancer, accounting for up to 90% of cases. In other geographic locations, different significant factors play a fundamental role in disease development, such as individual genetic predisposition, or exposure to other carcinogens such as radon gas, environmental pollution, occupational exposures, or specific infectious diseases. Comprehensive clinical and molecular characterization of lung cancer in recent decades has enabled us to distinguish different subtypes of lung cancer with distinct phenotypes, genotypes, immunogenicity, treatment responses, and survival rates. The ultimate goal is to prevent and individualize lung cancer management in each community and improve patient outcomes.

Mechanistic patterns and clinical implications of oncogenic tyrosine kinase fusions in human cancers

Tyrosine kinase (TK) fusions are frequently found in cancers, either as initiating events or as a mechanism of resistance to targeted therapy. Partner genes and exons in most TK fusions are typical and recurrent, but the underlying mechanisms and clinical implications of these patterns are poorly understood. Here, we investigated structures of > 8,000 kinase fusions and explore their generative mechanisms by applying newly developed experimental framework integrating high-throughput genome-wide gene fusion sequencing and clonal selection called Functionally Active Chromosomal Translocation Sequencing (FACTS). We discovered that typical oncogenic TK fusions recurrently seen in patients are selected from large pools of chromosomal rearrangements spontaneously occurring in cells based on two major determinants: active transcription of the fusion partner genes and protein stability. In contrast, atypical TK fusions that are rarely seen in patients showed reduced protein stability, decreased downstream oncogenic signaling, and were less responsive to inhibition. Consistently, patients with atypical TK fusions were associated with a reduced response to TKI therapies, as well as a shorter progression-free survival (PFS) and overall survival (OS) compared to patients with typical TK fusions. These findings highlight the principles of oncogenic TK fusion formation and their selection in cancers, with clinical implications for guiding targeted therapy.

AI-Derived CT Body Composition in Advanced Non-Small Cell Lung Cancer: A Multicohort Study

PURPOSE/OBJECTIVE(S)

The relationship between body composition (BC) and cancer outcomes is complex and incompletely understood. Previous research in non-small cell lung cancer (NSCLC) has been limited to small single-institution studies, which have yielded inconsistent results.

MATERIALS/METHODS

We conducted a comprehensive multicohort analysis to evaluate the impact of BC on overall survival (OS) in advanced NSCLC treated with systemic therapy. The analysis included data from the phase I/II CP1108 study (NSCLC Durvalumab cohort) and the chemotherapy arm of the phase III MYSTIC trial. We also analyzed data from Dana-Farber Cancer Institute (DFCI) cohorts receiving immunotherapy alone or in combination with chemotherapy. Baseline and follow-up (FU) CT scans were collected and analyzed using deep neural networks for automatic L3 slice selection and body compartment segmentation (skeletal muscle [SM], subcutaneous adipose tissue [SAT], and visceral adipose tissue [VAT]). We compared OS based on baseline BC measures or their change at the first FU scan. The impact of sarcopenia at baseline was evaluated in association with the delta metrics.

RESULTS

A total of 1865 NSCLC patients were analyzed, of which 222 were treated on CP1108, 257 were treated on MYSTIC, 870 received IO monotherapy at DFCI (DFCI-IO), and 516 received chemoimmunotherapy at DFCI (DFCI-CIO). The median ages were 65, 63, 66, and 65, respectively. A loss in SM mass >5%, as indicated by a change in L3 SM area, was significantly associated with poorer OS across all patient groups (median [months]: 5 vs. 19; p<0.001 for CP1108, 11 vs. 14; p = 0.03 for MYSTIC, 11 vs. 17; p<0.001 for DFCI-IO, and 12 vs. 22; p<0.001 for DFCI-CIO). This effect was driven by male patients, with a non-significant association (p>0.5) among female patients in the MYSTIC and DFCI-CIO cohorts. An increase in SAT density >5%, as quantified by the average CT attenuation in HU of the SAT compartment, was significantly linked to poorer OS in three patient groups (median [months]: 4 vs. 19; p<0.001 for CP1108, 10 vs. 17; p<0.001 for DFCI-IO, and 12 vs. 20; p = 0.003 for DFCI-CIO). This was primarily observed among female patients, with a non-significant association (p>0.5) among male patients in the DFCI-CIO cohort. On subgroup analysis, loss in SM mass had an impact on OS in patients with baseline sarcopenia (median [months] 5 vs. 22; p<0.001 for CP1108, 5 vs. 12; p = 0.03 for MYSTIC, 11 vs. 17; p<0.001 for DFCI IO, and 9 vs. 17; p = 0.003 for DFCI-CIO). Conversely, no association was observed between change in SM mass and OS in patients without sarcopenia at baseline in the MYSTIC and DFCI-IO cohorts.

CONCLUSION

Sarcopenia and loss in SM mass during systemic therapy for NSCLC are markers of poor outcome, especially in male patients. SAT density changes are also strongly associated with prognosis, particularly in female patients. Automated CT-derived BC measurements should be considered along with other risk factors in determining lung cancer prognosis and ability to tolerate oncologic treatments.

Amplification of Wild-Type RET Represents a Novel Molecular Subtype of Several Cancer Types With Clinical Response to Selpercatinib

PURPOSE

RET rearrangements and RET activating point mutations represent targetable genomic alterations in advanced solid tumors. However, the frequency and clinicopathologic characteristics of wild-type RET amplification in cancer and its potential role as a targetable oncogenic driver are not well-characterized.

METHODS

In two institutional cohorts of patients with solid cancers from the Dana-Farber Cancer Institute (DFCI) and Memorial Sloan Kettering Cancer Center (MSKCC) whose tumors underwent next-generation sequencing (NGS), the frequency and clinicopathologic features of wild-type RET amplification in the absence of RET rearrangements or activating mutations was assessed. The findings were validated using merged data from The Cancer Genome Atlas (TCGA), Genomics Evidence Neoplasia Information Exchange (GENIE), and China Pan-Cancer data sets.

RESULTS

The frequency of wild-type RET amplification across all solid cancers was 0.08% (26 of 32,505) in the DFCI cohort, 0.05% (26 of 53,152) in the MSKCC cohort, and 0.25% (71 of 28,623) in the cohort from TCGA, GENIE, and China Pan-Cancer. Cancer types with RET amplification included non-small-cell lung cancer (NSCLC), hepatobiliary cancer, prostate cancer, breast cancer, and others. The median RET copy number in RET-amplified cases was 7.5 (range, 6-36) in the DFCI cohort and 5.7 (range, 4-27.7) in the MSKCC cohort. Among 11 RET-amplified NSCLCs, eight had no other concurrent driver mutations. Finally, we report on a 69-year-old man with recurrent NSCLC harboring high-level wild-type RET amplification (22-28 copies) as the only identified putative genomic driver who experienced both a systemic and intracranial confirmed response to the RET inhibitor selpercatinib.

CONCLUSION

Amplification of wild-type RET represents a novel, targetable molecular subset of cancer.

Clinicopathologic, Genomic, and Immunophenotypic Landscape of ATM Mutations in Non-Small Cell Lung Cancer

PURPOSE

ATM is the most commonly mutated DNA damage and repair gene in non-small cell lung cancer (NSCLC); however, limited characterization has been pursued.

EXPERIMENTAL DESIGN

Clinicopathologic, genomic, and treatment data were collected for 5,172 patients with NSCLC tumors which underwent genomic profiling. ATM IHC was performed on 182 NSCLCs with ATM mutations. Multiplexed immunofluorescence was performed on a subset of 535 samples to examine tumor-infiltrating immune cell subsets.

RESULTS

A total of 562 deleterious ATM mutations were identified in 9.7% of NSCLC samples. ATM-mutant (ATMMUT) NSCLC was significantly associated with female sex (P = 0.02), ever smoking status (P < 0.001), non-squamous histology (P = 0.004), and higher tumor mutational burden (DFCI, P < 0.0001; MSK, P < 0.0001) compared with ATM-wild-type (ATMWT) cases. Among 3,687 NSCLCs with comprehensive genomic profiling, co-occurring KRAS, STK11, and ARID2 oncogenic mutations were significantly enriched among ATMMUT NSCLCs (Q < 0.05), while TP53 and EGFR mutations were enriched in ATMWT NSCLCs. Among 182 ATMMUT samples with ATM IHC, tumors with nonsense, insertions/deletions, or splice site mutations were significantly more likely to display ATM loss by IHC (71.4% vs. 28.6%; P < 0.0001) compared with tumors with only predicted pathogenic missense mutations. Clinical outcomes to PD-(L)1 monotherapy (N = 1,522) and chemo-immunotherapy (N = 951) were similar between ATMMUT and ATMWT NSCLCs. Patients with concurrent ATM/TP53 mutations had significantly improved response rate and progression-free survival with PD-(L)1 monotherapy.

CONCLUSIONS

Deleterious ATM mutations defined a subset of NSCLC with unique clinicopathologic, genomic, and immunophenotypic features. Our data may serve as resource to guide interpretation of specific ATM mutations in NSCLC.

Charge neutralized low energy beam transport at Brookhaven 200 MeV linac

The H(-) magnetron source provides about 100 mA H(-) beam to be match into the radio-frequency quadrupole accelerator. As H(-) beam traverses through low energy transport, it ionizes the residual gas and electrons are repelled and positive ions are trapped in the beam, due to negative potential of the beam, providing charge neutralization for the H(-) beam. The neutralization time for the critical density depends upon the background gas and its pressure. Critical density for xenon gas at 35 keV is about 43 times smaller than that of hydrogen and stripping cross section is only 5 times than that of hydrogen gas. We are using xenon gas to reduce neutralization time and to improve transmission through the 200 MeV linac. We are also using pulse nitrogen gas to improve transmission and stability of polarized H(-) beam from optically pumped polarized ion source.

Linac4 H⁻ ion sources

CERN's 160 MeV H(-) linear accelerator (Linac4) is a key constituent of the injector chain upgrade of the Large Hadron Collider that is being installed and commissioned. A cesiated surface ion source prototype is being tested and has delivered a beam intensity of 45 mA within an emittance of 0.3 π ⋅ mm ⋅ mrad. The optimum ratio of the co-extracted electron- to ion-current is below 1 and the best production efficiency, defined as the ratio of the beam current to the 2 MHz RF-power transmitted to the plasma, reached 1.1 mA/kW. The H(-) source prototype and the first tests of the new ion source optics, electron-dump, and front end developed to minimize the beam emittance are presented. A temperature regulated magnetron H(-) source developed by the Brookhaven National Laboratory was built at CERN. The first tests of the magnetron operated at 0.8 Hz repetition rate are described.

Investigation of ISIS and Brookhaven National Laboratory ion source electrodes after extended operation

Linac4 accelerator of Centre Européen de Recherches Nucléaires is under construction and a RF-driven H(-) ion source is being developed. The beam current requirement for Linac4 is very challenging: 80 mA must be provided. Cesiated plasma discharge ion sources such as Penning or magnetron sources are also potential candidates. Accelerator ion sources must achieve typical reliability figures of 95% and above. Investigating and understanding the underlying mechanisms involved with source failure or ageing is critical when selecting the ion source technology. Plasma discharge driven surface ion sources rely on molybdenum cathodes. Deformation of the cathode surfaces is visible after extended operation periods. A metallurgical investigation of an ISIS ion source is presented. The origin of the deformation is twofold: Molybdenum sputtering by cesium ions digs few tenths of mm cavities while a growth of molybdenum is observed in the immediate vicinity. The molybdenum growth under hydrogen atmosphere is hard and loosely bound to the bulk. It is, therefore, likely to peel off and be transported within the plasma volume. The observation of the cathode, anode, and extraction electrodes of the magnetron source operated at BNL for two years are presented. A beam simulation of H(-), electrons, and Cs(-) ions was performed with the IBSimu code package to qualitatively explain the observations. This paper describes the operation conditions of the ion sources and discusses the metallurgical analysis and beam simulation results.

Ion optics of RHIC electron beam ion source

RHIC electron beam ion source has been commissioned to operate as a versatile ion source on RHIC injection facility supplying ion species from He to Au for Booster. Except for light gaseous elements RHIC EBIS employs ion injection from several external primary ion sources. With electrostatic optics fast switching from one ion species to another can be done on a pulse to pulse mode. The design of an ion optical structure and the results of simulations for different ion species are presented. In the choice of optical elements special attention was paid to spherical aberrations for high-current space charge dominated ion beams. The combination of a gridded lens and a magnet lens in LEBT provides flexibility of optical control for a wide range of ion species to satisfy acceptance parameters of RFQ. The results of ion transmission measurements are presented.

Development of electron beam ion source charge breeder for rare isotopes at Californium Rare Isotope Breeder Upgrade

Recently, the Californium Rare Isotope Breeder Upgrade (CARIBU) to the Argonne Tandem Linac Accelerator System (ATLAS) was commissioned and became available for production of rare isotopes. Currently, an electron cyclotron resonance ion source is used as a charge breeder for CARIBU beams. To further increase the intensity and improve the purity of neutron-rich ion beams accelerated by ATLAS, we are developing a high-efficiency charge breeder for CARIBU based on an electron beam ion source (EBIS). The CARIBU EBIS charge breeder will utilize the state-of-the-art EBIS technology recently developed at Brookhaven National Laboratory (BNL). The electron beam current density in the CARIBU EBIS trap will be significantly higher than that in existing operational charge-state breeders based on the EBIS concept. The design of the CARIBU EBIS charge breeder is nearly complete. Long-lead components of the EBIS such as a 6-T superconducting solenoid and an electron gun have been ordered with the delivery schedule in the fall of 2011. Measurements of expected breeding efficiency using the BNL Test EBIS have been performed using a Cs(+) surface ionization ion source for external injection in pulsed mode. In these experiments we have achieved ∼70% injection∕extraction efficiency and breeding efficiency into the most abundant charge state of ∼17%.

Polarized proton collisions at 205 GeV at RHIC

The Brookhaven Relativistic Heavy Ion Collider (RHIC) has been providing collisions of polarized protons at a beam energy of 100 GeV since 2001. Equipped with two full Siberian snakes in each ring, polarization is preserved during acceleration from injection to 100 GeV. However, the intrinsic spin resonances beyond 100 GeV are about a factor of 2 stronger than those below 100 GeV making it important to examine the impact of these strong intrinsic spin resonances on polarization survival and the tolerance for vertical orbit distortions. Polarized protons were first accelerated to the record energy of 205 GeV in RHIC with a significant polarization measured at top energy in 2005. This Letter presents the results and discusses the sensitivity of the polarization survival to orbit distortions.

Observation of a hybrid spin resonance

A new type of spin depolarization resonance has been observed at the Brookhaven Alternating Gradient Synchrotron (AGS). This spin resonance is identified as a strong closed-orbit sideband around the dominant intrinsic spin resonance. The strength of the resonance was proportional to the 9th harmonic component of the horizontal closed orbit and proportional to the vertical betatron oscillation amplitude. This "hybrid" spin resonance cannot be overcome by the partial snake at the AGS, but it can be corrected by the harmonic orbit correctors.