The Kaiser Permanente Research Bank Cancer Cohort: a collaborative resource to improve cancer care and survivorship

Background

The Kaiser Permanente Research Bank (KPRB) is collecting biospecimens and surveys linked to electronic health records (EHR) from approximately 400,000 adult KP members. Within the KPRB, we developed a Cancer Cohort to address issues related to cancer survival, and to understand how genetic, lifestyle and environmental factors impact cancer treatment, treatment sequelae, and prognosis. We describe the Cancer Cohort design and implementation, describe cohort characteristics after 5 years of enrollment, and discuss future directions.

Methods

Cancer cases are identified using rapid case ascertainment algorithms, linkage to regional or central tumor registries, and direct outreach to KP members with a history of cancer. Enrollment is primarily through email invitation. Participants complete a consent form, survey, and donate a blood or saliva sample. All cancer types are included.

Results

As of December 31, 2020, the cohort included 65,225 cases (56% female, 44% male) verified in tumor registries. The largest group was diagnosed between 60 and 69 years of age (31%) and are non-Hispanic White (83%); however, 10,076 (16%) were diagnosed at ages 18–49 years, 4208 (7%) are Hispanic, 3393 (5%) are Asian, and 2389 (4%) are Black. The median survival time is 14 years. Biospecimens are available on 98% of the cohort.

Conclusions

The KPRB Cancer Cohort is designed to improve our understanding of treatment efficacy and factors that contribute to long-term cancer survival. The cohort’s diversity - with respect to age, race/ethnicity and geographic location - will facilitate research on factors that contribute to cancer survival disparities.

Semi-quantitative, high throughput analysis of SARS-CoV-2 neutralizing antibodies: Measuring the level and duration of immune response antibodies post infection/vaccination

The question associated with efficacy and longevity of SARS-CoV-2 protection post-vaccination is paramount. The cPass surrogate virus neutralization test (sVNT) has gained popularity globally as a dual application assay for: 1. Accurate SARS-CoV-2 population surveillance (seroprevalence) analysis and 2. Revealing the presence of antibodies that block and effectively neutralize the interaction between the SARS-CoV-2 receptor binding domain and the host cell ACE2 receptor in recovered or vaccinated individuals. This study describes an approach for accurate quantification of neutralizing antibodies using the cPass sVNT with an automated workflow on the Tecan EVO and Dynex Agility platforms that is applicable to other liquid handling systems. This methodology was used to assess the stability of SARS-CoV-2 neutralizing antibodies between freeze/thaw and refrigerated sample storage conditions. Furthermore, a subset of twenty-five samples from SARS-CoV-2 infected/recovered individuals revealed a 600-fold difference in the neutralizing antibody response where low titers were represented in about half of the samples. Finally, pre- and post-vaccination samples were tested for neutralizing antibodies using the qualitative and semi-quantitative cPass sVNT protocols revealing undetectable or relatively low levels after the first vaccine dose and a decline in levels longitudinally over the months following the second dose. This wide range in neutralizing (blocking) antibodies from both natural infection and vaccination supports a differential immune response that may be attributed to several physiological and genetic factors underlining the potential for measuring SARS-CoV-2 neutralizing antibody titer levels post-vaccination to help ensure robust and prolonged immunity.

Exploring molecular pathways of triple-negative breast cancer

Triple-negative breast cancer (TNBC) is an aggressive breast cancer subtype with a high rate of proliferation and metastasis, as well as poor prognosis for advanced-stage disease. Although TNBC was previously classified together with basal-like and BRCA1/2-related breast cancers, genomic profiling now shows that there is incomplete overlap, with important distinctions associated with each subtype. The biology of TNBC is still poorly understood; therefore, to define the relative contributions of major cellular pathways in TNBC, we have studied its molecular signature based on analysis of gene expression. Comparisons were then made with normal breast tissue. Our results suggest the existence of molecular networks in TNBC, characterized by explicit alterations in the cell cycle, DNA repair, nucleotide synthesis, metabolic pathways, NF-κB signaling, inflammatory response, and angiogenesis. Moreover, we also characterized TNBC as a cancer of mixed phenotypes, suggesting that TNBC extends beyond the basal-like molecular signature and may constitute an independent subtype of breast cancer. The data provide a new insight into the biology of TNBC.

Molecular signature and pathway analysis of human primary squamous and adenocarcinoma lung cancers

Non-small cell lung cancer (NSCLC) is the most common type of lung cancer, with a poor response to chemotherapy and low survival rate. This unfavorable treatment response is likely to derive from both late diagnosis and from complex, incompletely understood biology, and heterogeneity among NSCLC subtypes. To define the relative contributions of major cellular pathways to the biogenesis of NSCLC and highlight major differences between NSCLC subtypes, we studied the molecular signatures of lung adenocarcinoma (ADC) and squamous cell carcinoma (SCC), based on analysis of gene expression and comparison of tumor samples with normal lung tissue. Our results suggest the existence of specific molecular networks and subtype-specific differences between lung ADC and SCC subtypes, mostly found in cell cycle, DNA repair, and metabolic pathways. However, we also observed similarities across major gene interaction networks and pathways in ADC and SCC. These data provide a new insight into the biology of ADC and SCC and can be used to explore novel therapeutic interventions in lung cancer chemoprevention and treatment.

Abstract P6-04-12: Pathway Analysis of Primary Human Triple-Negative Breast Cancers

BACKGROUND: Breast cancer is a complex, heterogeneous disease due to vast differences in cellular origin, genetic mutations, metastatic potential, and disease progression. Triple-negative breast cancer (TNBC) is a subtype defined by negative expression of estrogen receptor, progesterone receptor, and human epidermal growth factor receptor-2. Because of its aggressive nature and poor prognosis, TNBC has gained recent attention within the oncology community. Tissue expression profiling with microarrays is a robust and straightforward method to study molecular features of TNBC at a systems level. The goal of this project was to further understand the pathogenesis of TNBC through comprehensive characterization of molecular and pathway signatures, based on analysis of freshly frozen and paraffin-embedded primary tumors from 20 TNBC patients, compared with syngeneic normal breast samples.

METHODS: Microarrary profiling of quadruplet sets of samples (freshly frozen and paraffin-embedded; 80 samples total) was conducted using the Affymetrix Human Gene 1.0 ST array. The differential expression profile of cancer vs. syngeneic normal tissue was calculated for each patient, as well as for combined samples, using the unpaired t-test. Pathway analyses based on gene expression profiling were performed using Pathway Studio (Ariadne Genomics, Inc). Functional enrichment was performed using Fisher's Exact test and Mann-Whitney test.

RESULTS: This analysis demonstrated that TNBC is characterized by a distinct molecular signature which includes genes and pathways of DNA repair, cell cycle, and energy production. Several DNA repair genes were upregulated by at least 2.3-fold, including CHEK1, BLM, NEIL3, PARP1, FANCI, FANCD2 and EXO1 (P <.0001 for each). While several genes in excision-repair pathways (DDB2, RPA1, XAB2 and RAB23A) were downregulated, most genes involved in homologous recombination (BRCA1, BRCA2, RAD54B, RAD51, and RAD51L1), DNA repair synthesis (POLQ and PCNA), and DNA mismatch repair (MLH1, MSH3, PMS1 and PMS2) were upregulated. Analysis of the PARP1 pathway revealed that most upstream and downstream neighbors of PARP1 were significantly upregulated between 2- and 4.5-fold in TNBC. Consistent with previous observations, PARP1 was significantly upregulated by 2.5-fold (P < .0001) in TNBC. Genes involved with cell cycle checkpoint control were also significantly altered, including 4.4-fold, 3.6-fold, and 6.8-fold upregulation of CCNB1, CDC2, and TOP2A, respectively (P < .0001 for each). Of genes involved in metabolic pathways, those involved in purine, folate and pyrimidine metabolism demonstrated changes consistent with active proliferation of TNBC cells. In addition, expression patterns related to inflammation (leukocyte migration, lymphocyte activation, macrophage chemotaxis) and angiogenesis were observed. This finding is consistent with previously described activation of the NFkB pathway and suggestive of an inflammatory component in the pathogenesis of TNBC. CONCLUSIONS : TNBC appears to be characterized by distinct alterations in DNA repair, cell cycle regulation, and metabolism, thus providing a molecular basis for identifying novel therapeutic strategies for this disease.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P6-04-12.