Transcriptional and epigenetic regulators of human CD8+ T cell function identified through orthogonal CRISPR screens.

Clinical response to adoptive T cell therapies is associated with the transcriptional and epigenetic state of the cell product. Thus, discovery of regulators of T cell gene networks and their corresponding phenotypes has potential to improve T cell therapies. Here we developed pooled, epigenetic CRISPR screening approaches to systematically profile the effects of activating or repressing 120 transcriptional and epigenetic regulators on human CD8+ T cell state. We found that BATF3 overexpression promoted specific features of memory T cells and attenuated gene programs associated with cytotoxicity, regulatory T cell function, and exhaustion. Upon chronic antigen stimulation, BATF3 overexpression countered phenotypic and epigenetic signatures of T cell exhaustion. Moreover, BATF3 enhanced the potency of CAR T cells in both in vitro and in vivo tumor models and programmed a transcriptional profile that correlates with positive clinical response to adoptive T cell therapy. Finally, we performed CRISPR knockout screens that defined cofactors and downstream mediators of the BATF3 gene network.

Spectrometric Analysis of Dantrolene Sodium.

Dantrolene sodium is a direct-acting skeletal muscle relaxant. Dantrolene sodium for injection is indicated, along with suitable supportive measures, for the management of sudden, severe hypermetabolism of skeletal muscle typical of malignant hyperthermia crises in patients of any age. The formulation scanned in this work was designed to be injected intravenously. Intra-lot and inter-lot variability in the spectra of REVONTO™ (dantrolene sodium) was measured in the Drug Quality Study (DQS) using Fourier transform near-infrared spectrometry (FTNIR). Spectra of 69 vials from lot 20REV01A contained two groups (n1=56 vials, n2=13 vials) when scanned with an FTNIR. The two groups of spectra in lot 20REV01A were found to be 66.7 SDs apart using a subcluster detection test, suggesting that the two groups were manufactured differently. As a result, all available samples of dantrolene were examined. A library of spectra of 141 vials of dantrolene from 4 lots were found to contain 3 separate groups, also suggesting that different vials contain different materials.

Quality Variations in Thyrotropin Alfa.

Thyrotropin alfa is a heterodimeric glycoprotein containing human thyroid stimulating hormone (TSH). It is used as an adjunctive diagnostic tool for serum thyroglobulin (Tg) testing with or without radioiodine imaging in the follow-up of patients with well-differentiated thyroid cancer who have previously undergone thyroidectomy. Inter-lot variability in the Fourier transform near-infrared spectra of 30 samples obtained from four separate lots of Thyrogen® was detected in the Drug Quality Study (DQS). The vials fell into two distinct groups (rtst = 0.90, rlim= 0.98, p=0.02). In addition, one vial of the 30 (3%) appeared 4.7 multidimensional SDs from all of the other vials, suggesting that it also represents a different material.

Orthogonal CRISPR screens to identify transcriptional and epigenetic regulators of human CD8 T cell function.

The clinical response to adoptive T cell therapies is strongly associated with transcriptional and epigenetic state. Thus, technologies to discover regulators of T cell gene networks and their corresponding phenotypes have great potential to improve the efficacy of T cell therapies. We developed pooled CRISPR screening approaches with compact epigenome editors to systematically profile the effects of activation and repression of 120 transcription factors and epigenetic modifiers on human CD8+ T cell state. These screens nominated known and novel regulators of T cell phenotypes with BATF3 emerging as a high confidence gene in both screens. We found that BATF3 overexpression promoted specific features of memory T cells such as increased IL7R expression and glycolytic capacity, while attenuating gene programs associated with cytotoxicity, regulatory T cell function, and T cell exhaustion. In the context of chronic antigen stimulation, BATF3 overexpression countered phenotypic and epigenetic signatures of T cell exhaustion. CAR T cells overexpressing BATF3 significantly outperformed control CAR T cells in both in vitro and in vivo tumor models. Moreover, we found that BATF3 programmed a transcriptional profile that correlated with positive clinical response to adoptive T cell therapy. Finally, we performed CRISPR knockout screens with and without BATF3 overexpression to define co-factors and downstream factors of BATF3, as well as other therapeutic targets. These screens pointed to a model where BATF3 interacts with JUNB and IRF4 to regulate gene expression and illuminated several other novel targets for further investigation.

Spectral Intra-Lot and Inter-Lot Variability in Carfilzomib.

Carfilzomib is a prescription injectable drug approved for use by the FDA as an antineoplastic agent, part of a drug class of medications known as proteasome inhibitors, and used to stop and slow the growth and progression of cancer cells within the body. The drug is approved as an agent to treat multiple myeloma. It is provided as a single-use vial that contains 60 mg of carfilzomib as a sterile, white to off-white lyophilized cake or powder. Intra-lot and inter-lot variability in the spectra of carfilzomib vials was detected in the Drug Quality Study (DQS) using Fourier transform near-infrared spectrometry (FTNIR). One of 12 vials of lot 1143966 manufactured for Onyx Pharmaceuticals, Inc. appeared 4.7 multidimensional standard deviations (SDs) from the other 11 vials in a 3-D space formed by the first 3 principal components, which captured 81% of the total spectral variation. Spectra of 168 vials from 18 lots in the spectral library formed two groups in the 3-D space formed by the first 3 principal components. One group contained 155 vials and the other group contained 13 vials. The 2 groups had different locations and scales using a subcluster detection test at p=0.02.

Potential Process Control Issues with Pemetrexed.

Pemetrexed is a folate analog metabolic inhibitor used in treatment of locally advanced or metastatic nonsquamous non-small cell lung cancer and for mesothelioma. Intra-lot and inter-lot variability in the spectra of ALIMTA® was detected in the Drug Quality Study (DQS) using Fourier transform near-infrared spectrometry (FTNIR). One vial of 12 (8%) sampled from lot S20I013A appeared 3.0 multidimensional SDs from the other vials, suggesting that it represents a different material. Consequently, additional spectra from other lots were analyzed. Spectra of 147 vials from 23 lots in the spectral library contained 14 vials that were outside the main group (26.4 SDs using a subcluster detection test), suggesting that the 14 library vials (9.5% of the total) also contain differing materials.

Patient-derived micro-organospheres enable clinical precision oncology.

Patient-derived xenografts (PDXs) and patient-derived organoids (PDOs) have been shown to model clinical response to cancer therapy. However, it remains challenging to use these models to guide timely clinical decisions for cancer patients. Here, we used droplet emulsion microfluidics with temperature control and dead-volume minimization to rapidly generate thousands of micro-organospheres (MOSs) from low-volume patient tissues, which serve as an ideal patient-derived model for clinical precision oncology. A clinical study of recently diagnosed metastatic colorectal cancer (CRC) patients using an MOS-based precision oncology pipeline reliably assessed tumor drug response within 14 days, a timeline suitable for guiding treatment decisions in the clinic. Furthermore, MOSs capture original stromal cells and allow T cell penetration, providing a clinical assay for testing immuno-oncology (IO) therapies such as PD-1 blockade, bispecific antibodies, and T cell therapies on patient tumors.

Neoadjuvant and Adjuvant Systemic Therapy for Early-Stage Non-small-Cell Lung Cancer.

Approximately a third of patients with non-small-cell lung cancer (NSCLC) present with surgically resectable disease. Patients who undergo surgical resection are at a high risk of relapse, and neoadjuvant and adjuvant chemotherapy improves disease-free survival (DFS) and overall survival (OS). The outcomes with neoadjuvant and adjuvant chemotherapy are similar, and both are used in clinical practice. Recent trials investigated the role of immunotherapy and targeted therapy in patients with early-stage disease. A phase III trial of adjuvant atezolizumab compared with standard of care (SOC) in patients with resected stage II or III disease and PD-L1 expression of 1% or greater, and a second trial of adjuvant pembrolizumab compared with placebo in patients with stage IB-III (regardless of tumor proportion score PD-L1 expression), both demonstrated an improvement in DFS. In the neoadjuvant setting, results of a phase III trial of chemotherapy and nivolumab compared with chemotherapy alone revealed an improvement in pathological complete response rate and event-free survival in patients with stage IB-IIIA disease. Finally, for epidermal growth factor receptor (EGFR) mutant NSCLC, a phase III trial of osimertinib compared with SOC revealed an improvement in DFS. The results of these and ongoing trials illustrate the integration of immunotherapy and targeted therapies into the treatment paradigm of patients with surgically resected NSCLC and have led to FDA and EMA approvals in selected populations. Neoadjuvant trials have investigated novel endpoints such as major and complete pathological response, which have the potential to serve as surrogate endpoints for future trials.

Clinical Trials with Biologic Primary Endpoints in Immuno-oncology: Concepts and Usage.

Clinical trials that have a pharmacokinetic or a pharmacodynamic immunologic mechanism of action-based primary outcome could substantially improve the validity and efficiency of early development of immuno-oncology agents. Here, we outline different trial design options in this area, review examples from the literature and their unique immunologic aspects, and highlight how these trials have been underutilized. We illustrate how new technologies and translationally focused approaches can be successfully used to develop different classes of immunotherapeutic agents.

Immune Checkpoint Inhibitors in the Aged.

PURPOSE OF REVIEW: Large phase III trials have established the benefit of checkpoint blockade across multiple tumor types, but patient representation is limited in some subgroups including the aged population. There are several changes in the immune system that occur with age (termed immunosenescence) that could potentially limit efficacy in aged populations. RECENT FINDINGS: Despite the concerns stated above, available evidence from prospective trials, retrospective cohorts, and registry data suggest that elderly patients achieve similar benefit with immune checkpoint blockade in comparison to the general population and do not have increased toxicity. However, as patients age, they are at higher risk of developing a decline in multiple physiologic systems (including the immune system) and reduced ability to recover from illness. Clinical evidence shows that patients who have a poor performance status have inferior outcomes and limited clinical benefit from checkpoint blockade. Clinicians should take an individualized approach that accounts for each patient's health status rather than considering age alone when determining who should be offered checkpoint blockade therapy.

Biomarkers of Immune Checkpoint Blockade Response in Triple-Negative Breast Cancer.

OPINION STATEMENT: Immune checkpoint blockade (ICB) has revolutionized the treatment landscape across multiple solid tumor types. In triple-negative breast cancer (TNBC), clinical benefit for the addition of ICB to chemotherapy has been shown in both the metastatic and early stage disease settings. A minority of patients with TNBC will truly benefit from ICB, with many tumors unlikely to respond, and ICB can cause additional toxicities for patients to incur. In clinical practice, ICB-based regimens are emerging as standard-of-care treatment options in TNBC subpopulations. Atezolizumab in combination with nab-paclitaxel is recommended as first-line treatment for patients with PD-L1-positive metastatic TNBC. Clinical trials are needed to confirm this benefit and evaluate if additional biomarkers may allow for improved patient selection. Trials investigating ICB in early-stage breast cancer show promise for the benefit of combination ICB with neoadjuvant chemotherapy. However, longer follow-up is required before ICB can be considered as standard-of-care treatment in the early stage setting. In both metastatic and early stage TNBC, novel biomarkers to improve patient selection are now under investigation. These include multiplex IHC to profile immune cell subtypes (such as tumor infiltrating lymphocytes) or RNA gene expression profiling to detect signatures suggestive of a T-cell-inflamed microenvironment. Detecting somatic mutations through tumor next-generation DNA sequencing may predict resistance mechanisms or suggest sensitivity to ICB monotherapy or in combination with other forms of systemic therapy. These biomarker platforms may allow for a more granular analysis of immune activity and should be further investigated in prospective studies with the aim of personalizing ICB-focused therapies in TNBC.

Activated Coagulation Time and Hepcon Protamine Titration Device to Manage Unfractionated Heparin During Cardiopulmonary Bypass in a Hemophilia A Patient on Emicizumab.

In the perioperative management of patients with hemophilia A, emicizumab prevents the accurate measurement of common clotting assays, including the activated clotting time (ACT), which is essential for high-dose heparin monitoring during cardiopulmonary bypass surgery. The authors describe the successful perioperative management of a hemophilia A patient on maintenance emicizumab who, following a non-ST myocardial infarction, underwent cardiopulmonary bypass grafting surgery with heparin monitoring using both the ACT and heparin levels from the Hepcon protamine titration device. Postoperatively, the patient was transitioned to recombinant factor VIII replacement therapy. In hemophilia A patients on emicizumab who require heparin titration on cardiopulmonary bypass surgery, the ACT, combined with Hepcon heparin levels, may be used to complete the surgery successfully without excessive bleeding or morbidity.