Building a vertically integrated genomic learning health system: The biobank at the Colorado Center for Personalized Medicine

Precision medicine initiatives across the globe have led to a revolution of repositories linking large-scale genomic data with electronic health records, enabling genomic analyses across the entire phenome. Many of these initiatives focus solely on research insights, leading to limited direct benefit to patients. We describe the biobank at the Colorado Center for Personalized Medicine (CCPM Biobank) that was jointly developed by the University of Colorado Anschutz Medical Campus and UCHealth to serve as a unique, dual-purpose research and clinical resource accelerating personalized medicine. This living resource currently has more than 200,000 participants with ongoing recruitment. We highlight the clinical, laboratory, regulatory, and HIPAA-compliant informatics infrastructure along with our stakeholder engagement, consent, recontact, and participant engagement strategies. We characterize aspects of genetic and geographic diversity unique to the Rocky Mountain region, the primary catchment area for CCPM Biobank participants. We leverage linked health and demographic information of the CCPM Biobank participant population to demonstrate the utility of the CCPM Biobank to replicate complex trait associations in the first 33,674 genotyped individuals across multiple disease domains. Finally, we describe our current efforts toward return of clinical genetic test results, including high-impact pathogenic variants and pharmacogenetic information, and our broader goals as the CCPM Biobank continues to grow. Bringing clinical and research interests together fosters unique clinical and translational questions that can be addressed from the large EHR-linked CCPM Biobank resource within a HIPAA- and CLIA-certified environment.

Abstract 3448: The IV STING agonist, TAK-676, enhances immune-mediated anti-tumor activity of radiation in syngeneic mouse models

Robust interferon (IFN) signaling is integral for productive immune-mediated anti-tumor responses; however, impaired IFN signaling has been linked to checkpoint inhibitor (CPI) resistance. The cyclic GMP-AMP Synthase (cGAS)-STimulator of InterferoN Genes (STING) pathway is an essential regulator of IFN signaling in response to aberrant cytosolic DNA, including from tumors, and has emerged as an attractive therapeutic target. TAK-676 is a systemically delivered novel synthetic STING agonist that binds to and activates STING along with downstream IFN signaling, which is currently being evaluated in a Phase 1 dose escalation study of patients with advanced tumors (NCT04420884). In addition, focal radiation treatment of tumors leads to cell death coupled with innate cell activation and antigen presentation, suggesting that combining STING activation with radiotherapy (+/- anti-PD1) could lead to improved tumor control. The combination of TAK-676 with radiation +/- anti-PD1 was explored in immunocompetent EMT6 tumor-bearing BALB/c mice. Fractionated focal radiation (8Gy X 3) followed by TAK-676 (1 mg/kg dosed Q3D X 3) resulted in complete regression (CR) of tumors in 6/8 mice, whereas no CRs were detected in groups treated with radiation alone or with TAK-676 as a single agent. These observations suggest that addition of TAK-676 to a radiation regimen leads to enhanced tumor growth control compared to either treatment alone. In contrast, adding anti-PD1 to TAK-676 + fractionated radiation did not further increase tumor growth inhibition in this anti-PD1 resistant tumor model, with 5/8 CRs detected. Rechallenge of mice achieving CRs with EMT6 tumors resulted in rejection of the tumors in 3/5 and 4/5 mice from the double and triple combinations regimens, respectively, suggesting establishment of immunologic memory following primary challenge and treatment. Pharmacodynamic studies found both TAK-676 (1mg/kg) and fractionated radiation (8Gy X 3) monotherapy led to increased T cell accumulation and activation in the lymph nodes. However, only TAK-676 with fractionated radiation enhanced local IFN-γ production within the tumor, suggesting an enhanced adaptive immune response to this combination that drives the increase in observed efficacy. These studies support the evaluation of TAK-676 in combination with pembrolizumab following fractionated stereotactic body radiation therapy (SBRT) in a dose escalation clinical trial in patients with select advanced tumors (NCT04879849).

Citation Format: Vicky A. Appleman, Allison J. Berger, Emily R. Roberts, Angel E. Maldonado-Lopez, Michelle L. Ganno, Camilla I. Christensen, Tiquella Hatten, Yosuke Sato, Michael H. Shaw, Karim S. Malek, Neil B. Lineberry, Adnan O. Abu-Yousif, Richard C. Gregory. The IV STING agonist, TAK-676, enhances immune-mediated anti-tumor activity of radiation in syngeneic mouse models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3448.

TAK-676: A Novel Stimulator of Interferon Genes (STING) Agonist Promoting Durable IFN-dependent Antitumor Immunity in Preclinical Studies

Oncology therapies targeting the immune system have improved patient outcomes across a wide range of tumor types, but resistance due to an inadequate T-cell response in a suppressive tumor microenvironment (TME) remains a significant problem. New therapies that activate an innate immune response and relieve this suppression may be beneficial to overcome this hurdle. TAK-676 is a synthetic novel stimulator of interferon genes (STING) agonist designed for intravenous administration. Here we demonstrate that TAK-676 dose-dependently triggers activation of the STING signaling pathway and activation of type I interferons. Furthermore, we show that TAK-676 is a highly potent modulator of both the innate and adaptive immune system and that it promotes the activation of dendritic cells, natural killer cells, and T cells in preclinical models. In syngeneic murine tumor models in vivo, TAK-676 induces dose-dependent cytokine responses and increases the activation and proliferation of immune cells within the TME and tumor-associated lymphoid tissue. We also demonstrate that TAK-676 dosing results in significant STING-dependent antitumor activity, including complete regressions and durable memory T-cell immunity. We show that TAK-676 is well tolerated, exhibits dose-proportional pharmacokinetics in plasma, and exhibits higher exposure in tumor. The intravenous administration of TAK-676 provides potential treatment benefit in a broad range of tumor types. Further study of TAK-676 in first-in-human phase I trials is ongoing.

Significance

TAK-676 is a novel systemic STING agonist demonstrating robust activation of innate and adaptive immune activity resulting in durable antitumor responses within multiple syngeneic tumor models. Clinical investigation of TAK-676 is ongoing.

Clinical implementation of pharmacogenomics via a health system-wide research biobank: the University of Colorado experience

In recent years, the genomics community has witnessed the growth of large research biobanks, which collect DNA samples for research purposes. Depending on how and where the samples are genotyped, biobanks also offer the potential opportunity to return actionable genomic results to the clinical setting. We developed a preemptive clinical pharmacogenomic implementation initiative via a health system-wide research biobank at the University of Colorado. Here, we describe how preemptive return of clinical pharmacogenomic results via a research biobank is feasible, particularly when coupled with strong institutional support to maximize the impact and efficiency of biobank resources, a multidisciplinary implementation team, automated clinical decision support tools, and proactive strategies to engage stakeholders early in the clinical decision support tool development process.

The Emergency Medicine Specimen Bank: An Innovative Approach To Biobanking In Acute Care

The Emergency Medicine Specimen Bank (EMSB) was developed to facilitate precision medicine in acute care. The EMSB is a biorepository of clinical health data and biospecimens collected from all adult English- or Spanish-speaking individuals who are able and willing to provide consent and are treated at the UCHealth-University of Colorado Hospital Emergency Department. The EMSB is the first acute care biobank that seeks to enroll all patients, with all conditions who present to the ED. Acute care biobanking presents many challenges that are unique to acute care settings such as providing informed consent in a uniquely stressful and fast-paced environment and collecting, processing, and storing samples for tens of thousands of patients per year. Here, we describe the process by which the EMSB overcame these challenges and was integrated into clinical workflow allowing for operation 24 hours a day, 7 days a week at a reasonable cost. Other institutions can implement this template, further increasing the power of biobanking research to inform treatment strategies and interventions for common and uncommon phenotypes in acute care settings.

Identification and characterization of HIV-specific resident memory CD8+ T cells in human lymphoid tissue

Current paradigms of CD8⁺ T cell-mediated protection in HIV infection center almost exclusively on studies of peripheral blood, which is thought to provide a window into immune activity at the predominant sites of viral replication in lymphoid tissues (LTs). Through extensive comparison of blood, thoracic duct lymph (TDL), and LTs in different species, we show that many LT memory CD8⁺ T cells bear phenotypic, transcriptional, and epigenetic signatures of resident memory T cells (T_RMs). Unlike their circulating counterparts in blood or TDL, most of the total and follicular HIV-specific CD8⁺ T cells in LTs also resemble T_RMs Moreover, high frequencies of HIV-specific CD8⁺ T_RMs with skewed clonotypic profiles relative to matched blood samples are present in LTs of individuals who spontaneously control HIV replication in the absence of antiretroviral therapy (elite controllers). Single-cell RNA sequencing analysis confirmed that HIV-specific T_RMs are enriched for effector-related immune genes and signatures compared with HIV-specific non-T_RMs in elite controllers. Together, these data indicate that previous studies in blood have largely failed to capture the major component of HIV-specific CD8⁺ T cell responses resident within LTs.

Collapse of Cytolytic Potential in SIV-Specific CD8+ T Cells Following Acute SIV Infection in Rhesus Macaques

Poor maintenance of cytotoxic factor expression among HIV-specific CD8+ T cells, in part caused by dysregulated expression of the transcription factor T-bet, is associated with HIV disease progression. However, the precise evolution and context in which CD8+ T cell cytotoxic functions become dysregulated in HIV infection remain unclear. Using the rhesus macaque (RM) SIV infection model, we evaluated the kinetics of SIV-specific CD8+ T cell cytolytic factor expression in peripheral blood, lymph node, spleen, and gut mucosa from early acute infection through chronic infection. We identified rapid acquisition of perforin and granzyme B expression in SIV-specific CD8+ T cells in blood, secondary lymphoid tissues and gut mucosa that collapsed rapidly during the transition to chronic infection. The evolution of this expression profile was linked to low expression of T-bet and occurred independent of epitope specificity, viral escape patterns and tissue origin. Importantly, during acute infection SIV-specific CD8+ T cells that maintained T-bet expression retained the ability to express granzyme B after stimulation, but this relationship was lost in chronic infection. Together, these data demonstrate the loss of cytolytic machinery in SIV-specific CD8+ T cells in blood and at tissue sites of viral reservoir and active replication during the transition from acute to chronic infection. This phenomenon occurs despite persistent high levels of viremia suggesting that an inability to maintain properly regulated cytotoxic T cell responses in all tissue sites enables HIV/SIV to avoid immune clearance, establish persistent viral reservoirs in lymphoid tissues and gut mucosa, and lead ultimately to immunopathogenesis and death.

The role of mitochondria in the development and progression of lung cancer

The influence of mitochondria in human health and disease is a rapidly expanding topic in the scientific literature due to their integral roles in cellular death and survival. Mitochondrial biology and alterations in function were first linked to cancer in the 1920s with the discovery of the Warburg effect. The utilization of aerobic glycolysis in ATP synthesis was the first of many observations of metabolic reprogramming in cancer.

Mitochondrial dysfunction in cancer has expanded to include defects in mitochondrial genomics and biogenesis, apoptotic signaling and mitochondrial dynamics. This review will focus on the role of mitochondria and their influence on cancer initiation, progression and treatment in the lung.

Therapeutic targeting of NOTCH signaling ameliorates immune-mediated bone marrow failure of aplastic anemia

Notch1 signaling sustains the proinflammatory behavior of Th1 cells, implicated in the development of aplastic anemia in humans and mice.

Severe aplastic anemia (AA) is a bone marrow (BM) failure (BMF) disease frequently caused by aberrant immune destruction of blood progenitors. Although a Th1-mediated pathology is well described for AA, molecular mechanisms driving disease progression remain ill defined. The NOTCH signaling pathway mediates Th1 cell differentiation in the presence of polarizing cytokines, an action requiring enzymatic processing of NOTCH receptors by γ-secretase. Using a mouse model of AA, we demonstrate that expression of both intracellular NOTCH1^IC and T-BET, a key transcription factor regulating Th1 cell differentiation, was increased in spleen and BM-infiltrating T cells during active disease. Conditionally deleting Notch1 or administering γ-secretase inhibitors (GSIs) in vivo attenuated disease and rescued mice from lethal BMF. In peripheral T cells from patients with untreated AA, NOTCH1^IC was significantly elevated and bound to the TBX21 promoter, showing NOTCH1 directly regulates the gene encoding T-BET. Treating patient cells with GSIs in vitro lowered NOTCH1^IC levels, decreased NOTCH1 detectable at the TBX21 promoter, and decreased T-BET expression, indicating that NOTCH1 signaling is responsive to GSIs during active disease. Collectively, these results identify NOTCH signaling as a primary driver of Th1-mediated pathogenesis in AA and may represent a novel target for therapeutic intervention.

Adverse effects of homeopathy: a systematic review of published case reports and case series - comment by Tournier et al

Linked Comment: Jackson. Int J Clin Pract 2013; 67: 385. Linked Comment: Walach et al. Int J Clin Pract 2013; 67: 385–6. Linked Comment: Posadzki and Ernst. Int J Clin Pract 2013; 67: 386–7. Linked Comment: Grimes. Int J Clin Pract 2013; 67: 387. Linked Comment: Posadzki and Ernst. Int J Clin Pract 2013; 67: 389.

Mississippi public health nurses and midwives: a partnership that worked

At the turn of the century maternal and infant mortality rates were high in this southern state. Untrained midwives conducted many of the deliveries. Initial support for locating and training midwives by public health nurses was provided by the American Red Cross and the United States Public Health Services. Later, funding from a philanthropic organization (Rockefeller International Foundation) provided a mechanism that brought Mississippi public health nurses and midwives to a partnership that endured for over a half a century, and contributed to better maternal-infant health care outcomes for that state.