Early Noninvasive Detection of Response to Targeted Therapy in Non-Small Cell Lung Cancer

With the advent of precision oncology, there is an urgent need to develop improved methods for rapidly detecting responses to targeted therapies. Here, we have developed an ultrasensitive measure of cell-free tumor load using targeted and whole-genome sequencing approaches to assess responses to tyrosine kinase inhibitors in patients with advanced lung cancer. Analyses of 28 patients treated with anti-EGFR or HER2 therapies revealed a bimodal distribution of cell-free circulating tumor DNA (ctDNA) after therapy initiation, with molecular responders having nearly complete elimination of ctDNA (>98%). Molecular nonresponders displayed limited changes in ctDNA levels posttreatment and experienced significantly shorter progression-free survival (median 1.6 vs. 13.7 months, P < 0.0001; HR = 66.6; 95% confidence interval, 13.0-341.7), which was detected on average 4 weeks earlier than CT imaging. ctDNA analyses of patients with radiographic stable or nonmeasurable disease improved prediction of clinical outcome compared with CT imaging. These analyses provide a rapid approach for evaluating therapeutic response to targeted therapies and have important implications for the management of patients with cancer and the development of new therapeutics.Significance: Cell-free tumor load provides a novel approach for evaluating longitudinal changes in ctDNA during systemic treatment with tyrosine kinase inhibitors and serves an unmet clinical need for real-time, noninvasive detection of tumor response to targeted therapies before radiographic assessment.See related commentary by Zou and Meyerson, p. 1038.

Abstract 4596: Early noninvasive prediction of response to targeted therapy in non-small cell lung cancer

There is an unmet need for improved methods of rapidly identifying responses to targeted therapies. Liquid biopsy approaches have potential as early biomarkers of response based on noninvasive, real-time monitoring of disease burden. We have used the ultrasensitive targeted error correction sequencing (TEC-Seq) approach to analyze 58 cancer driver genes in patients with metastatic non-small cell lung cancer undergoing treatment with targeted tyrosine kinase inhibitors. As a proof-of-principle study, liquid biopsies were obtained from sixteen patients immediately prior to treatment, 6-22 days after treatment, and at serial timepoints until disease progression. Tumor derived alterations and copy number changes were directly detected in plasma and tracked over timepoints analyzed. Based on the dynamics of cell-free circulating tumor DNA (ctDNA) mutations identified, we developed a noninvasive measure of cell-free clonal tumor load (cfTL) to evaluate real-time response to treatment. These analyses revealed that patients with a radiographic response to therapy had a significant drop in cfTL from an average mutant allele fraction of 3.59% to 0.13% within 6-22 days (P &lt; 0.05) as well as in the number of detectable mutations and aneuploidy scores, while radiographic non-responders had limited to no changes. Analyses of residual cfTL 6-22 days after treatment stratified patients into ctDNA responders and ctDNA non-responders. ctDNA responders had improved progression-free survival (12.4 vs 1.7 months, P &lt; 0.001), which was detected on average 38 days earlier and was as predictive as CT imaging. These analyses provide an approach for rapid evaluation of response to targeted therapies and have important clinical implications for the management of cancer patients.

Citation Format: Jillian A. Phallen, Alessandro Leal, Brian D. Woodward, Patrick M. Forde, Jarushka Naidoo, Kristen Marrone, Julie Brahmer, Jacob Fiksel, Doreen N. Palsgrove, Stephen Cristiano, Daniel Bruhm, Elizabeth Weihe, Vilmos Adleff, Parissa Keshavarzian, Valsamo Anagnostou, Robert B. Scharpf, Victor E. Velculescu, Hatim Husain. Early noninvasive prediction of response to targeted therapy in non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4596.

Direct detection of early-stage cancers using circulating tumor DNA

Early detection and intervention are likely to be the most effective means for reducing morbidity and mortality of human cancer. However, development of methods for noninvasive detection of early-stage tumors has remained a challenge. We have developed an approach called targeted error correction sequencing (TEC-Seq) that allows ultrasensitive direct evaluation of sequence changes in circulating cell-free DNA using massively parallel sequencing. We have used this approach to examine 58 cancer-related genes encompassing 81 kb. Analysis of plasma from 44 healthy individuals identified genomic changes related to clonal hematopoiesis in 16% of asymptomatic individuals but no alterations in driver genes related to solid cancers. Evaluation of 200 patients with colorectal, breast, lung, or ovarian cancer detected somatic mutations in the plasma of 71, 59, 59, and 68%, respectively, of patients with stage I or II disease. Analyses of mutations in the circulation revealed high concordance with alterations in the tumors of these patients. In patients with resectable colorectal cancers, higher amounts of preoperative circulating tumor DNA were associated with disease recurrence and decreased overall survival. These analyses provide a broadly applicable approach for noninvasive detection of early-stage tumors that may be useful for screening and management of patients with cancer.

Abstract LB-246: Detection of circulating tumor DNA in early stage cancers

Early detection is a major goal for reducing mortality of human cancer. However, non-invasive detection of early stage tumors has remained a challenge. We have developed an approach called Targeted Error Correction Sequencing (TEC-Seq) for ultra-sensitive analyses of circulating cell-free tumor DNA (ctDNA). This methodology involves in-solution targeted capture of multiple regions of the genome and deep sequencing (~30,000x) of cell-free DNA fragments. Laboratory and bioinformatic methods were optimized to enrich for rare ctDNA molecules and to reduce potential amplification, sequencing, and contamination errors. We have used this approach to examine 58 cancer related genes, and demonstrated a limit of detection of mutant to wild-type DNA of 0.05% and a specificity &gt;99.999% across targeted regions of interest. We applied this method to analyze plasma from healthy individuals as well as over 200 individuals with breast, lung, colorectal and ovarian cancers. Analysis of plasma from 44 healthy individuals revealed no tumor-related somatic mutations and identified alterations in genes related to myelodysplasia in a subset of cases. Among patients with cancer, we detected measurable ctDNA in 56%, 71%, 57%, and 56% of patients with early stage (I and II) breast, colorectal, lung and ovarian cancer. Over three quarters of patients with late stage (III and IV) disease had detectable ctDNA among all cases analyzed. Analyses of mutations in the circulation revealed a high concordance with alterations in the independently analyzed tumors of these patients. These analyses provide a widely applicable, ultra-sensitive, and non-invasive method for detection of ctDNA, and have important implications for detection of early stage disease and management of patients with cancer.

Citation Format: Jillian A. Phallen, Mark Sausen, Vilmos Adleff, Alessandro Leal, Jacob Fiksel, Carolyn Hruban, Savannah Speir, Eniko Papp, Valsamo Anagnostou, Mai-Britt W. Orntoft, Thomas Reinert, Brian D. Woodward, Derek Murphy, Sonya Parpart-Li, David Riley, Monica Nesselbush, Naomi Sengamalay, Andrew Georgiadis, Rob Scharpf, Qing K. Li, Sian Jones, Samuel Angiuoli, Joost Huiskens, Cornelis Punt, Nicole van Grieken, Remond Fijneman, Gerrit Meijer, Hatim Husain, Luis Diaz, Torben Ørntoft, Hans J. Nielsen, Claus L. Anderson, Victor E. Velculescu. Detection of circulating tumor DNA in early stage cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-246. doi:10.1158/1538-7445.AM2017-LB-246

New Targets in Non-Small Cell Lung Cancer

With the implementation of genomic technologies into clinical practice, we have examples of the predictive benefit of targeted therapy for oncogene-addicted cancer and identified molecular dependencies in non-small cell lung cancer. The clinical success of tyrosine kinase inhibitors against epidermal growth factor receptor and anaplastic lymphoma kinase activation has shifted treatment emphasize the separation of subsets of lung cancer and genotype-directed therapy. Advances have validated oncogenic driver genes and led to the development of targeted agents. This review highlights treatment options, including clinical trials for ROS1 rearrangement, RET fusions, NTRK1 fusions, MET exon skipping, BRAF mutations, and KRAS mutations.

The proportion of CD45RA(+)CD62L(+) (quiescent-phenotype) T cells within the CD8(+) subset increases in advanced weight loss in the protein- or energy-deficient weanling mouse

Male and female C57BL/6J mice, initially 19 d old, had free access to a complete purified diet, were fed this diet in restricted daily quantities, or had free access to a low-protein diet. Three separate studies were conducted with feeding periods of 14, 9 or 6 d (n = 7-8 per dietary group and feeding period; 6 d: restricted intake and age-matched controls only). A zero-time control group (19 d old) was included in each study. Malnourished mice lost approximately 2% of initial body weight daily. Naïve-phenotype (quiescent) CD8(+) T cells of the blood, spleen and mesenteric lymph nodes were identified on the basis of surface coexpression of CD45RA and CD62L. Relative to age-matched controls, the percentage of naïve-phenotype CD8(+) T cells was high in energy-restricted groups after 9 d and 14 d of weight loss and in the protein-restricted groups after 14 d (P < or = 0.05). No ontogenetic change was apparent (age-matched vs. zero-time control). Other studies have demonstrated depression in cell-mediated immune competence in both malnutrition models within the first week of weight loss. An overabundance of quiescent-phenotype T cells within the involuted CD8(+) compartment may contribute to established immune depression but not to its initiation in weight loss pathologies.

Overabundance of CD45RA(+) (quiescent-phenotype) cells within the involuted CD4(+) T-cell population follows initiation of immune depression in energy-deficient weanling mice and reflects involution exclusive to the CD45RA(-) subset

Previous studies have identified an overabundance of quiescent-phenotype (CD45RA(+)) CD4(+) T cells throughout the lymphoid system of weanling mice at an advanced stage of food intake restriction mimicking marasmus. The objective of this investigation was to determine the timing of this phenomenon relative to the development of depression in cell-mediated immune competence. Two experiments were conducted in which male and female weanling C57BL/6J mice, initially 19 d of age, either were permitted free access to a complete purified diet or were subjected to restricted intake of this diet, producing loss of 1.5-2% of initial body weight daily. In the first experiment, feeding periods of 3, 6, 9, 12 and 14 d were examined, and a zero-time control group (19 d old) was also included. Expression of CD45RA was assessed by flow cytometry in CD4(+) T cells from the blood, spleen and mesenteric lymph nodes. Despite reduction in CD4(+) T-cell numbers, evident in all three lymphoid compartments of the malnourished mice by d 6, energy-restricted mice maintained the numbers of CD4(+)CD45RA(+) T cells at the level found in the zero-time control group. Consequently, the malnourished group exhibited a high percentage of CD4(+) T cells expressing CD45RA by d 9 in the blood and mesenteric nodes and by d 12 in the spleen. In the second study, malnourished and age-matched control groups were sensitized to sheep red blood cells on d 3 and energy-restricted mice exhibited depression in the delayed hypersensitivity response to this antigen when assessed on d 9 after challenge 24 h previously. Energy deficiency pathology includes a shift toward CD4(+) T cell quiescence that may contribute to ongoing immunodepression without being involved in its initiation. Remarkably, this imbalance develops because involution of the CD4(+) subset in the energy-deficient mice is confined to the CD45RA(-) population.

The CD4/CD8 ratio in the blood does not reflect the response of this index in secondary lymphoid organs of weanling mice in models of protein-energy malnutrition known to depress thymus-dependent immunity

A low ratio of cellular numbers within CD4+ (helper/inducer) relative to CD8+ (suppressor/cytotoxic) thymic lymphocyte subsets (low CD4/CD8 ratio) is widely accepted as fundamental to the depression in thymus-dependent immunocompetence associated with wasting protein-energy malnutrition (PEM). The objective of this investigation, therefore was to determine the CD4/CD8 ratio in peripheral lymphoid compartments of diverse murine models of protein-energy malnutrition which produce systemic wasting (loss of approximately 1.8% of initial body weight per day), lymphoid involution and (as shown in many previous studies) depression in thymus-dependent immunocompetence. In the first of two experiments, male and female weanling mice of disparate inbred strains, CBA/J and C57BL/6J, were allocated to a zero-time control group (23- and 19-d-old, respectively), or to groups fed for 14 d as follows: ad libitum intake of a complete purified diet (19% crude protein, 17 kJ/g gross energy), restricted intake of the complete diet, or ad libitum intake of an isocaloric low protein diet (0.6% crude protein). In a supplementary experiment, (0.6% crude protein). In a supplementary experiment, male and female C57BL/6J weanling mice were fed the complete diet or the low protein diet for either 6 or 21 d. CD4+ and CD8+ thymic lymphocytes were enumerated by flow cytometry in mononuclear cell suspensions from blood, spleen and mesenteric lymph nodes. A low CD4/CD8 ratio is common in the blood in wasting protein-energy malnutrition, but appears uncharacteristic of the profoundly involuted lymphoid organs which generate acquired immune responses. The CD4/CD8 ratio is irrelevant to the thymus-dependent immunoincompetence previously demonstrated in the rodent models used in this investigation.

Expansion of the humoral effector cell compartment of both systemic and mucosal immune systems in a weanling murine model which duplicates critical features of human protein-energy malnutrition

A direct comparison of systemic (spleen) and mucosal (intestine) antibody-producing systems was made in weanling male C57BL/6J mice subjected to wasting protein-energy malnutrition (PEM) by means of a low-protein protocol known to duplicate immunological and physiological features of human malnutrition. ELISA revealed low concentrations of biliary and gut lumen immunoglobulin (Ig) A in malnourished mice concomitantly with a high concentration of blood IgA. The low-protein model, therefore, exhibited fidelity to human protein-energy malnutrition in its influence on the concentrations of the mucosal Ig, IgA, in critical biological fluids. The number of IgA-, IgM- and IgG-containing cells was estimated morphometrically on a per organ basis. The low-protein protocol supported expansion in numbers of mucosal IgA-containing cells (18 x relative to a zero-time control group) and of splenic IgG-containing cells (135x), albeit an attenuated expansion in comparison with that of well-nourished control animals (132x and 571x respectively relative to zero-time controls). Up to terminal differentiation of Ig-containing cells, systemic and mucosal antibody-producing systems exhibited similarly remarkable resistance to wasting malnutrition. Epithelial transport of IgA may be an aspect of the mucosal antibody response which is particularly sensitive to PEM.

The CD45RA+ (quiescent) cellular phenotype is overabundant relative to the CD45RA- phenotype within the involuted splenic T cell population of weanling mice subjected to wasting protein-energy malnutrition

The objective of this investigation was to determine whether an imbalance between naive- and memory-phenotype cells occurs within CD4+ and/or CD8+ splenic T cell subsets in models of protein-energy malnutrition (PEM) which produce wasting disease (loss of approximately 1.6% of body weight per day for 14 d) and profound depression in thymus-dependent immunity. Male and female weanling mice of disparate inbred strains, CBA/J and C57BL/6J, were allocated to the following groups: zero-time control (23 d old and 19 d old, respectively), ad libitum intake of a complete purified diet (19% crude protein, 17 kJ/g gross energy), restricted intake of the complete diet, and (C57BL/6J, only) ad libitum intake of an isocaloric low protein diet (0.6% crude protein). Surface expression of isoforms of CD45, a component of the T cell receptor complex, as well as of the accessory molecule, CD2, were assessed by flow cytometry of splenic mononuclear cell suspensions. Both major T cell subsets in the malnourished groups contained a significantly higher proportion of cells expressing the surface marker, CD45RA, than was found in the spleen cells of the control groups. CD45RA+ (naive-phenotype) T cells represent the extreme of quiescence and stringent activation requirements among thymic lymphocytes. The results provide the first clear evidence of a T cell subset imbalance in PEM which is consistent with depression in acquired immunity and which occurs, apart from antigenic challenge, in a site wherein immune responses take place. The T cell receptor complex may emerge as a focal point of the depressive influence of PEM on the competence of thymic lymphocytes.

Direct evidence that primary acquired cell-mediated immunity is less resistant than is primary thymus-dependent humoral immunity to the depressive influence of wasting protein-energy malnutrition in weanling mice

Wasting protein-energy malnutrition (PEM) was induced in male C57BL/6J mice fed a low-protein diet ad libitum from 23 to 37 d of age. In comparison with a complete diet, the low-protein formulation reduced delayed hypersensitivity to sheep red blood cells (SRBCs) assessed on day 14 of feeding by measuring increased footpad thickness (mean +/- SD: 4 +/- 4% vs 22 +/- 8%, P less than 0.01), after immunization on day 9, and after challenge with SRBCs on day 13. By contrast, the low-protein diet did not affect the anti-SRBC hemagglutinin titer (8.3 +/- 2.2 vs 9.1 +/- 1.1, P greater than 0.30) despite profound reduction in numbers of splenic plasma cells secreting IgM-class anti-SRBCs (7.3 +/- 3.1 vs 49.9 +/- 23.8 x 10(-3), P less than 0.001), after immunization on day 9 and assessment on day 14. Thus, direct experimental evidence, previously altogether lacking, is provided in support of the concept, central to nutritional immunology, that acquired cell-mediated immunity is less resistant than is systemic humoral immunity to the depressive influence of pre-adolescent, wasting PEM.

Enhancement of primary systemic acquired immunity by exogenous triiodothyronine in wasted, protein-energy malnourished weanling mice

The objectives of this investigation were to expand information regarding the types of acquired immune responses that can be stimulated by triiodothyronine (T3) supplements in wasting protein-energy malnutrition (PEM) and to determine whether T3 can exert its enhancing influence on acquired immunity in PEM against diverse genetic backgrounds. Two experiments were conducted with weanling C57BL/6J mice. Animals were allowed ad libitum access for 14 d to a nutritionally complete purified diet (C), an isoenergetic low protein (0.6%) formulation (LP) or the low protein diet containing 0.2 microgram T3/g (LPT3). The LP diet produced wasting as judged by weight loss and carcass composition. This diet also depressed both the antibody response to sheep red blood cells (Experiment 1) and the complete major histocompatibility complex-disparate skin graft rejection response (Experiment 2). The LPT3-fed mice experienced wasting at least equivalent in magnitude to that of animals fed LP, but they exhibited significantly more vigorous responses than LP-fed animals in both immune reactions examined. In conjunction with previous results obtained using the CBA/J strain of mouse, the results show that not only humoral (antibody) responses but also at least some cell-mediated responses can be improved by T3 supplements in wasting PEM. Moreover, this influence on acquired immunity is apparent in at least two genetically unrelated mouse strains, thus increasing confidence in its basic biological significance.

Depression of thymus-dependent immunity in wasting protein-energy malnutrition does not depend on an altered ratio of helper (CD4+) to suppressor (CD8+) T cells or on a disproportionately large atrophy of the T-cell relative to the B-cell pool

We report cell numbers within major subsets of lymphocytes in the spleen, mesenteric nodes, and recirculating pool of weanling mice subjected to protein-energy malnutrition (PEM). PEM and thymus (T)-dependent immunodepression were induced in male C57BL/6J mice by a low-protein (LP) diet fed ad libitum. Recirculating lymphocyte numbers were estimated by enumerating labeled and unlabeled cells after equilibration of a known number of fluorescein isothiocyanate-labeled C57BL/6J donor lymphocytes within well-nourished or LP recipients. Involution of the recirculating lymphocyte pool of the LP group was proportionately less than the lymphoid atrophy of the spleen and mesenteric nodes. The LP protocol exerted no influence on the ratio of helper (CD4+) to suppressor (CD8+) T cells and increased the ratio of T cells to B cells in the secondary lymphoid organs and recirculating pool. These results challenge two established concepts: that T-dependent immunodepression in PEM depends on a reduced CD4(+)-CD8+ ratio and that PEM induces greater involution within the T-cell system than within the B-cell system.