Clinical validation of an immunohistochemistry-based CanAssist-Breast test for distant recurrence prediction in hormone receptor-positive breast cancer patients

CanAssist‐Breast (CAB) is an immunohistochemistry (IHC)‐based prognostic test for early‐stage Hormone Receptor (HR+)‐positive breast cancer patients. CAB uses a Support Vector Machine (SVM) trained algorithm which utilizes expression levels of five biomarkers (CD44, ABCC4, ABCC11, N‐Cadherin, and Pan‐Cadherin) and three clinical parameters such as tumor size, grade, and node status as inputs to generate a risk score and categorizes patients as low‐ or high‐risk for distant recurrence within 5 years of diagnosis. In this study, we present clinical validation of CAB. CAB was validated using a retrospective cohort of 857 patients. All patients were treated either with endocrine therapy or chemoendocrine therapy. Risk categorization by CAB was analyzed by calculating Distant Metastasis‐Free Survival (DMFS) and recurrence rates using Kaplan‐Meier survival curves. Multivariate analysis was performed to calculate Hazard ratios (HR) for CAB high‐risk vs low‐risk patients. The results showed that Distant Metastasis‐Free Survival (DMFS) was significantly different (P‐0.002) between low‐ (DMFS: 95%) and high‐risk (DMFS: 80%) categories in the endocrine therapy treated alone subgroup (n = 195) as well as in the total cohort (n = 857, low‐risk DMFS: 95%, high‐risk DMFS: 84%, P < 0.0001). In addition, the segregation of the risk categories was significant (P = 0.0005) in node‐positive patients, with a difference in DMFS of 12%. In multivariate analysis, CAB risk score was the most significant predictor of distant recurrence with hazard ratio of 3.2048 (P < 0.0001). CAB stratified patients into discrete risk categories with high statistical significance compared to Ki‐67 and IHC4 score‐based stratification. CAB stratified a higher percentage of the cohort (82%) as low‐risk than IHC4 score (41.6%) and could re‐stratify >74% of high Ki‐67 and IHC4 score intermediate‐risk zone patients into low‐risk category. Overall the data suggest that CAB can effectively predict risk of distant recurrence with clear dichotomous high‐ or low‐risk categorization.

Development of a Novel Proteomic Risk-Classifier for Prognostication of Patients With Early-Stage Hormone Receptor-Positive Breast Cancer

Use of proteomic strategies to identify a risk classifier that estimates probability of distant recurrence in early-stage hormone receptor (HR)-positive breast cancer is relevant to physiological cellular function and therefore to intrinsic tumor biology. We used a 298-sample retrospective training set to develop an immunohistochemistry-based novel risk classifier called CanAssist-Breast (CAB) which combines 5 prognostically relevant biomarkers and 3 clinico-pathological parameters to arrive at probability of distant recurrence within 5 years from diagnosis. Five selected biomarkers, namely, CD44, ABCC4, ABCC11, N-cadherin, and pan-cadherin, were chosen based on their role in tumor metastasis. The chosen biomarkers represent the hallmarks of cancer and are distinct from other proliferation and gene expression-based prognostic signatures. The 3 clinico-pathological parameters integrated into the machine learning-based CAB algorithm are tumor size, tumor grade, and node status. These features are used to calculate a "CAB risk score" that classifies patients into low- or high-risk groups and predicts probability of distant recurrence in 5 years. Independent clinical validation of CAB in a retrospective study comprising 196 patients indicated that distant metastasis-free survival (DMFS) was significantly different in the 2 risk groups. The difference in DMFS between the low- and high-risk categories was 19% in the validation cohort (P = .0002). In multivariate analysis, CAB risk score was the most significant independent predictor of distant recurrence with a hazard ratio of 4.3 (P = .0003). CanAssist-Breast is a precise and unique machine learning-based proteomic risk-classifier that can assist in risk stratification of patients with early-stage HR+ breast cancer.

Abstract P3-08-10: Development and validation of a broad-based second generation multi marker “Morphometric IHC” test for optimal treatment planning of stage 1 and 2 breast cancer patients in low resource settings

Aims:

Assessment of 'risk of recurrence' in ER+ breast cancer patients based on clinical parameters and existing hormone receptor signaling pathway and/or proliferation based biomarkers is insufficient, leading to treatment of majority of patients with chemotherapy. First generation risk identification tests like OncotypeDx and Mammaprint are not impactful in India and SE Asia as are largely prognostic with limited chemotherapy-predictivity and are prohibitively expensive. A cost-effective 'predictive' test which will accurately estimate the 'risk of recurrence' for a 'broader' (node - & +) set of breast cancer patients in low resource settings is urgently required.

Materials and Methods:

Using a retrospective training cohort of 300 node– and node+ patients, we developed 'CanAssist-Breast'- a Morphometric Immunohistochemistry based test comprising 5 biomarkers plus three clinical parameters (Tumor size, grade and node status) to arrive at 'CanAssist-Breast Score'. The risk stratification model was developed using cutting edge support vector based machine learning technology. CanAssist-Breast Score stratifies patients into an all actionable 'low or high' risk for recurrence, with no intermediate zone. CanAssist-Breast biomarkers include cancer stem cell markers, Cadherins, and ATP transporter proteins - all critical players in the various steps of chemotherapy resistance leading to metastasis.

Results:

We validated CanAssist-Breast in accordance with EGAPP recommendations which require that prognostic tests be validated both analytically and clinically prior to being utilized in patients. Analytical validation experiments were performed to assess 'variation' in the outcome prediction due to critical IHC variables. We tested inter-pathologists, sample, operator and laboratory site variation and found high concordance in the outcome predictions across all variables, confirming the robustness and reproducibility of the test.

Extended clinical validation on 1000+ pre and post-menopausal cases shows NPV of 95%. The majority of patients in 'low risk' had Stage 2, Grade 2/3 disease over Stage 1, Grade 1 disease, demonstrating that CanAssist-Breast reclassifies patients who would be considered high risk clinically.

In a head-to-head pilot study of 100 patients with Oncotype Dx, CanAssist-Breast test had about 80% concordance with Oncotype in the 'low risk' category. Importantly, CanAssist-Breast correctly stratified few recurred cases as 'high risk' which were called 'low risk' by Oncotype Dx and thus were not treated with chemotherapy.

Conclusion:

In conclusion, we have developed a robust, accurate and low-cost prognostic test to predict risk of recurrence and enable optimal treatment planning in patients with early stage Breast Cancer.

Citation Format: SP S, Bakre MM, Ramkumar C, Basavaraj C, Attuluri A, Madhav L, Prakash C, Naidu N, Malpani S. Development and validation of a broad-based second generation multi marker “Morphometric IHC” test for optimal treatment planning of stage 1 and 2 breast cancer patients in low resource settings [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P3-08-10.

A Circulating microRNA Signature Predicts Age-Based Development of Lymphoma

Extensive epidemiological data have demonstrated an exponential rise in the incidence of non-Hodgkin lymphoma (NHL) that is associated with increasing age. The molecular etiology of this remains largely unknown, which impacts the effectiveness of treatment for patients. We proposed that age-dependent circulating microRNA (miRNA) signatures in the host influence diffuse large B cell lymphoma (DLBCL) development. Our objective was to examine tumor development in an age-based DLBCL system using an inventive systems biology approach. We harnessed a novel murine model of spontaneous DLBCL initiation (Smurf2-deficient) at two age groups: 3 and 15 months old. All Smurf2-deficient mice develop visible DLBCL tumor starting at 15 months of age. Total miRNA was isolated from serum, bone marrow and spleen and were collected for all age groups for Smurf2-deficient mice and age-matched wild-type C57BL/6 mice. Using systems biology techniques, we identified a list of 10 circulating miRNAs being regulated in both the spleen and bone marrow that were present in DLBCL forming mice starting at 3 months of age that were not present in the control mice. Furthermore, this miRNA signature was found to occur circulating in the blood and it strongly impacted JUN and MYC oncogenic signaling. In addition, quantification of the miRNA signature was performed via Droplet Digital PCR technology. It was discovered that a key miRNA signature circulates throughout a host prior to the formation of a tumor starting at 3 months old, which becomes further modulated by age and yielded calculation of a ‘carcinogenic risk score’. This novel age-based circulating miRNA signature may potentially be leveraged as a DLBCL risk profile at a young age to predict future lymphoma development or disease progression as well as for potential innovative miRNA-based targeted therapeutic strategies in lymphoma.

Smurf2 regulates hematopoietic stem cell self-renewal and aging

The age-dependent decline in the self-renewal capacity of stem cells plays a critical role in aging, but the precise mechanisms underlying this decline are not well understood. By limiting proliferative capacity, senescence is thought to play an important role in age-dependent decline of stem cell self-renewal, although direct evidence supporting this hypothesis is largely lacking. We have previously identified the E3 ubiquitin ligase Smurf2 as a critical regulator of senescence. In this study, we found that mice deficient in Smurf2 had an expanded hematopoietic stem cell (HSC) compartment in bone marrow under normal homeostatic conditions, and this expansion was associated with enhanced proliferation and reduced quiescence of HSCs. Surprisingly, increased cycling and reduced quiescence of HSCs in Smurf2-deficient mice did not lead to premature exhaustion of stem cells. Instead, HSCs in aged Smurf2-deficient mice had a significantly better repopulating capacity than aged wild-type HSCs, suggesting that decline in HSC function with age is Smurf2 dependent. Furthermore, Smurf2-deficient HSCs exhibited elevated long-term self-renewal capacity and diminished exhaustion in serial transplantation. As we found that the expression of Smurf2 was increased with age and in response to regenerative stress during serial transplantation, our findings suggest that Smurf2 plays an important role in regulating HSC self-renewal and aging.

Smurf2 suppresses B-cell proliferation and lymphomagenesis by mediating ubiquitination and degradation of YY1

About half of patients with diffuse large B-cell lymphoma (DLBCL) do not respond to or relapse soon after the standard chemotherapy, indicating a critical need to better understand the specific pathways perturbed in DLBCL for developing effective therapeutic approaches. Mice deficient in the E3 ubiquitin ligase Smurf2 spontaneously develop B-cell lymphomas that resemble human DLBCL with molecular features of germinal center or post-germinal center B cells. Here we show that Smurf2 mediates ubiquitination and degradation of YY1, a key germinal center transcription factor. Smurf2 deficiency enhances YY1-mediated transactivation of c-Myc and B-cell proliferation. Furthermore, Smurf2 expression is significantly decreased in primary human DLBCL samples, and low levels of Smurf2 expression correlate with inferior survival in DLBCL patients. The Smurf2-YY1-c-Myc regulatory axis represents a novel pathway perturbed in DLBCL that suppresses B-cell proliferation and lymphomagenesis, suggesting pharmaceutical targeting of Smurf2 as a new therapeutic paradigm for DLBCL.

Smurf2 regulates hematopoietic stem cell self-renewal and aging (HEM2P.256)

The age-dependent decline in the self-renewal capacity of stem cells plays a critical role in aging, but the precise mechanisms underlying this decline are not well understood. By limiting proliferative capacity, senescence is thought to play an important role in age-dependent decline of stem cell self-renewal, although direct evidence supporting this hypothesis is largely lacking. We have previously identified the E3 ubiquitin ligase Smurf2 as a critical regulator of senescence. In this study, we found that mice deficient in Smurf2 had an expanded hematopoietic stem cell (HSC) compartment in bone marrow under normal homeostatic conditions, and this expansion was associated with enhanced proliferation and reduced quiescence of HSCs. Surprisingly, increased cycling and reduced quiescence of HSCs in Smurf2-deficient mice did not lead to premature exhaustion of stem cells. Instead, HSCs in aged Smurf2-deficient mice had a significantly better repopulating capacity than aged wild-type HSCs, suggesting that decline in HSC function with age is Smurf2-dependent. Furthermore, Smurf2-deficient HSCs exhibited elevated long-term self-renewal capacity and diminished exhaustion in serial transplantation. As we found that the expression of Smurf2 was increased with age and in response to regenerative stress during serial transplantation, our findings suggest that Smurf2 plays an important role in regulating HSC self-renewal and aging.

Smurf2 mediates ubiquitination and degradation of YY1 to suppress B-cell proliferation and lymphomagenesis (P2181)

Current treatment of diffuse large B-cell lymphoma (DLBCL), the most common type of non-Hodgkin’s lymphoma, has improved patient survival significantly. However, 40-50% of DLBCL patients still die from this disease. There is a critical need to better understand the specific molecular pathways that are perturbed in DLBCL for the development of new therapeutic approaches. Using a mouse model deficient in the E3 ubiquitin ligase Smurf2, we show that Smurf2 deficiency increases the susceptibility of these mice to spontaneous B-cell lymphomagenesis. Lymphomas developed in Smurf2-deficient mice resemble human DLBCL with molecular features of germinal center B cells. We discover that Smurf2 mediates ubiquitination and degradation of YY1, a key germinal center transcription factor. Importantly, loss of Smurf2 enhances YY1-mediated transactivation of c-Myc and B-cell proliferation. Furthermore, we find that expression of Smurf2 is significantly decreased in primary human DLBCL samples compared to normal B cells. Importantly, low levels of Smurf2 expression correlate with poor survival prognosis in DLBCL patients. The Smurf2-YY1-c-Myc regulatory axis represents a novel pathway perturbed in DLBCL that suppresses B-cell proliferation and lymphomagenesis, and identifies Smurf2 as a new therapeutic paradigm for DLBCL.

Abstract 1994: Smurf2 mediates ubiquitination and degradation of YY1 to suppress B-cell proliferation and lymphomagenesis

Current treatment of diffuse large B-cell lymphoma (DLBCL), the most common type of non-Hodgkin's lymphoma, has improved patient survival significantly. However, 40-50% of DLBCL patients still die from this disease. There is a critical need to better understand the specific molecular pathways that are perturbed in DLBCL for the development of new and effective therapeutic approaches. We show that mice deficient in the E3 ubiquitin ligase Smurf2 spontaneously develop B-cell lymphomas that resemble human DLBCL with molecular features of germinal center B cells. We discover that Smurf2 mediates ubiquitination and degradation of YY1, a key germinal center transcription factor. Importantly, Smurf2 deficiency enhances YY1-mediated transactivation of c-Myc and B-cell proliferation. Furthermore, the expression of Smurf2 is significantly decreased in primary human DLBCL samples compared to normal B cells, and low levels of Smurf2 expression correlate with poor survival prognosis in DLBCL patients. The Smurf2-YY1-c-Myc regulatory axis represents a novel pathway perturbed in DLBCL that suppresses B-cell proliferation and lymphomagenesis, suggesting Smurf2 as a new therapeutic paradigm for DLBCL.

Citation Format: Charusheila Ramkumar, Hang Cui, Yahui Kong, Stephen Jones, Rachel Gerstein, Hong Zhang. Smurf2 mediates ubiquitination and degradation of YY1 to suppress B-cell proliferation and lymphomagenesis. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1994. doi:10.1158/1538-7445.AM2013-1994

Note: This abstract was not presented at the AACR Annual Meeting 2013 because the presenter was unable to attend.

Serial transplantation of bone marrow to test self-renewal capacity of hematopoietic stem cells in vivo

Hematopoietic stem cells (HSCs) have the ability to self-renew and replenish the blood and immune system for the life span of an individual. An age-associated decline in HSC function is responsible for the decreased immune function and increased incidence of myeloid diseases and anemia in the elderly. The changes in HSC function are thought to occur as the result of an intrinsic defect in the self-renewal potential of HSCs as they age. In this chapter, we describe a bone marrow serial transplantation protocol designed to test the self-renewal capacity of HSCs in vivo.

Smurf2 regulates the senescence response and suppresses tumorigenesis in mice

The E3 ubiquitin ligase Smurf2 mediates ubiquitination and degradation of several protein targets involved in tumorigenesis and induces senescence in human cells. However, the functional role of Smurf2 in tumorigenesis has not been fully evaluated. In this study, we generated a mouse model of Smurf2 deficiency to characterize the function of this E3 ligase in tumorigenesis. Smurf2 deficiency attenuated p16 expression and impaired the senescence response of primary mouse embryonic fibroblasts. In support of a functional role in controlling cancer, Smurf2 deficiency increased the susceptibility of mice to spontaneous tumorigenesis, most notably B-cell lymphoma. At a premalignant stage of tumorigenesis, we documented a defective senescence response in the spleens of Smurf2-deficient mice, consistent with a mechanistic link between impaired senescence regulation and increased tumorigenesis. Taken together, our findings offer the genetic evidence of an important tumor suppressor function for Smurf2.

The E3 ubiquitin ligase Smurf2 suppresses c-myc expression and B cell lymphoma in mice (74.4)

The NCI estimates in 2012 there will be 70,130 new cases and 18,940 deaths from non-Hodgkin’s lymphoma (NHL) in the US. Diffuse large B-cell lymphoma (DLBCL) is the most common NHL. This aggressive B-cell lymphoma is heterogeneous, with significant variation in response to treatment. Gene expression profiling identifies biologically distinct subtypes of DLBCL, which correlate with both response to treatment and survival. This suggests the critical importance of sub-type-specific targets in the diagnosis and treatment of DLBCL. The E3 ubiquitin ligase Smurf2 induces senescence in human cells, suggesting it is a tumor suppressor. We discovered that ~30% of mice deficient in Smurf2 develop NHLs with a post-germinal center phenotype resembling human DLBCL. B cells from healthy Smurf2-deficient mice exhibit enhanced proliferation and elevated expression of the oncogene c-myc. We find that Smurf2 mediates ubiquitination of a key transcription factor, which, when stabilized in Smurf2-deficient cells increases c-myc expression. This Smurf2-c-Myc axis represents a novel mechanism by which Smurf2 suppresses cell proliferation and lymphomagenesis. Analysis of gene expression databases reveals a significant decrease in Smurf2 expression in human DLBCL compared to normal B cells. Importantly, low level Smurf2 expression correlates with inferior overall survival in DLBCL patients. These data suggest that Smurf2 is a novel target in the diagnosis and potential treatment of human DLBCL.

Regulation of senescence in cancer and aging

Senescence is regarded as a physiological response of cells to stress, including telomere dysfunction, aberrant oncogenic activation, DNA damage, and oxidative stress. This stress response has an antagonistically pleiotropic effect to organisms: beneficial as a tumor suppressor, but detrimental by contributing to aging. The emergence of senescence as an effective tumor suppression mechanism is highlighted by recent demonstration that senescence prevents proliferation of cells at risk of neoplastic transformation. Consequently, induction of senescence is recognized as a potential treatment of cancer. Substantial evidence also suggests that senescence plays an important role in aging, particularly in aging of stem cells. In this paper, we will discuss the molecular regulation of senescence its role in cancer and aging. The potential utility of senescence in cancer therapeutics will also be discussed.

Abstract 2914: Mice deficient in Smurf2 exhibit increased spontaneous tumorigenesis

Smurf2, a HECT family E3 ubiquitin ligase has been shown to ubiquitinate and target for degradation of several proteins that promote tumorigenesis, including TGF-β receptors, Smad2/3, β-catenin, and Mad2. Furthermore, we have previously found that Smurf2 can induce senescence in early passage cells in culture. As senescence has been postulated to act as a tumor suppression mechanism, we hypothesize that Smurf2 functions as a tumor suppressor. To test this hypothesis, we generated a Smurf2-deficienct mouse strain using a gene trapping strategy, in which transcription of Smurf2 is compromised. The homozygous Smurf2-deficient mice were obtained with the expected Mendelian ratio after intercrossing of heterozygous mice, and they exhibited no obvious developmental defects. Analysis of mouse embryonic fibroblasts from these Smurf2-deficient mice revealed that they exhibited delayed senescence entry and consequently had an increased tendency to become immortalized in culture. Cohorts of Smurf2-deficient and wild-type mice were generated and monitored for spontaneous tumor development. In this ongoing study, 37% (13 out of 35) of the Smurf2-deficient mice, but none of the wild-type mice showed signs of morbidity after 14-month of age. The moribund Smurf2-deficient mice were found to have enlarged spleen, pale kidneys and liver, and/or enlarged lymph nodes. Histopathology analysis indicated that most of the tumors are lymphomas. In addition, adenocarcinoma of the small intestine was found in one Smurf2-deficient mouse. Collectively, our data suggest that Smurf2 is a tumor suppressor. Preliminary studies of the underlying molecular mechanism of tumorigenesis in Smurf2-deficient mice will be presented.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2914.

Abstract B50: Smurf2-deficient mice exhibit increased tumorigenesis

Smurf2, a HECT family E3 ubiquitin ligase has been shown to ubiquitinate and target for degradation several proteins that promote tumorigenesis, including TGF-β receptors, Smad2/3, β-catenin, and Mad2. Furthermore, we have found previously that Smurf2 can induce senescence in early passage cells in culture. As senescence has been postulated to act as a tumor suppression mechanism, we hypothesized that Smurf2 functions as a tumor suppressor. To test this hypothesis, we generated a Smurf2-deficienct mouse strain using a gene trapping strategy. The homozygous Smurf2-deficient mice were obtained with the expected Mendelian ratio after intercrossing of heterozygous mice, and they exhibited no obvious developmental defects. Analysis of mouse embryonic fibroblasts from these Smurf2-deficient mice revealed that they exhibited delayed senescence entry and consequently had an increased tendency to immortalize in culture. Cohorts of Smurf2-deficient and wild-type mice were monitored for spontaneous tumor development. In this ongoing study, 20% (7 out of 35) of the Smurf2-deficient mice, but none of the wild-type mice showed signs of morbidity after 14-months of age. The moribund Smurf2-deficient mice were found to have enlarged spleen, pale kidneys and liver, and/or enlarged lymph nodes. Histopathology analysis indicated that most of the tumors are lymphomas. In addition, we found adenocarcinoma of the intestine in one Smurf2-deficient mouse. Collectively, our data suggest that Smurf2 is a tumor suppressor. The investigation of the mechanism by which Smurf2 deficiency leads to tumorigenesis is ongoing.

Citation Information: Cancer Res 2009;69(23 Suppl):B50.

Influence of calcium, magnesium, or potassium ions on the formation and stability of emulsions prepared using highly hydrolyzed whey proteins

Oil-in-water emulsions (4 wt % soy oil) containing 4 wt % whey protein hydrolysate (WPH) (27% degree of hydrolysis) and different levels of calcium, magnesium, or potassium chloride were prepared in a two-stage homogenizer. Other emulsions containing 4 wt % WPH but including 0.35 wt % hydroxylated lecithin and different levels of the above minerals were similarly prepared. The formation and stability of these emulsions were determined by measuring oil droplet size distributions using laser light scattering and by confocal scanning laser microscopy and a gravity creaming test. Both lecithin-free and lecithin-containing emulsions showed no change in droplet size distributions with increasing concentration of potassium in the range 0-37.5 mM. In contrast, the diameter of emulsion droplets increased with increasing calcium or magnesium concentration >12.5 mM. Emulsions containing hydroxylated lecithin were more sensitive to the addition of calcium or magnesium than the lecithin-free emulsions. Storage of emulsions at 20 degrees C for 24 h further increased the diameter of droplets and resulted in extensive creaming in emulsions containing >25 mM calcium or magnesium. It appears that both flocculation and coalescence processes were involved in the destabilization of emulsions induced by the addition of divalent cations.