Immunotherapies for locally aggressive cancers

Improving surgical resection outcomes for locally aggressive tumors is key to inducing durable locoregional disease control and preventing progression to metastatic disease. Macroscopically complete resection of the tumor is the standard of care for many cancers, including breast, ovarian, lung, sarcoma, and mesothelioma. Advancements in cancer diagnostics are increasing the number of surgically eligible cases through early detection. Thus, a unique opportunity arises to improve patient outcomes with decreased recurrence rates via intraoperative delivery treatments using local drug delivery strategies after the tumor has been resected. Of the current systemic treatments (e.g., chemotherapy, targeted therapies, and immunotherapies), immunotherapies are the latest approach to offer significant benefits. Intraoperative strategies benefit from direct access to the tumor microenvironment which improves drug uptake to the tumor and simultaneously minimizes the risk of drug entering healthy tissues thereby resulting in fewer or less toxic adverse events. We review the current state of immunotherapy development and discuss the opportunities that intraoperative treatment provides. We conclude by summarizing progress in current research, identifying areas for exploration, and discussing future prospects in sustained remission.

Orthogonal inducible control of Cas13 circuits enables programmable RNA regulation in mammalian cells

RNA plays an indispensable role in mammalian cell functions. Cas13, a class of RNA-guided ribonuclease, is a flexible tool for modifying and regulating coding and non-coding RNAs, with enormous potential for creating new cell functions. However, the lack of control over Cas13 activity has limited its cell engineering capability. Here, we present the CRISTAL (Control of RNA with Inducible SpliT CAs13 Orthologs and Exogenous Ligands) platform. CRISTAL is powered by a collection (10 total) of orthogonal split inducible Cas13 effectors that can be turned ON or OFF via small molecules in multiple cell types, providing precise temporal control. Also, we engineer Cas13 logic circuits that can respond to endogenous signaling and exogenous small molecule inputs. Furthermore, the orthogonality, low leakiness, and high dynamic range of our inducible Cas13d and Cas13b enable the design and construction of a robust incoherent feedforward loop, leading to near-perfect and tunable adaptation response. Finally, using our inducible Cas13 effectors, we achieve simultaneous multiplexed control of multiple genes in vitro and in mice. Together, our CRISTAL design represents a powerful platform for precisely regulating RNA dynamics to advance cell engineering and elucidate RNA biology.

Engineered bacteria guide T cells to tumors

T cells and bacteria are engineered to work together to find and destroy tumor cells.

"Moderately Hypofractionated" Radiotherapy with a Simultaneously Integrated Boost for Synchronous Treatment of Prostate and Anorectal Cancer

PURPOSE/OBJECTIVE(S)

Data suggest safety and efficacy of 1.8-2.0 Gy per day radiotherapy (RT) with sequential boost regimens for patients with synchronous prostate and anorectal cancers. Emergence of 25-28 fraction (fx) prostate cancer RT regimens has enabled simultaneously integrated boost techniques to treat the prostate and anorectum (HypoRT), but limited reports exist to support the safety or efficacy of this approach. We aimed to assess oncologic outcomes and patient-reported outcomes (PRO)- and physician-reported adverse effects (AEs) of HypoRT for patients with synchronous prostate and anorectal cancers.

MATERIALS/METHODS

This was a retrospective cohort study of patients synchronously diagnosed with prostate and rectal cancer or anal canal squamous cell carcinoma (ASCC) treated with a HypoRT technique and concurrent chemotherapy between 2014-2022. Outcomes included prostate cancer biochemical recurrence (BCR), anorectal cancer recurrence, progression-free (PFS) and overall survival (OS). Acute and late gastrointestinal (GI) and genitourinary (GU) AEs and PRO were prospectively collected using common terminology criteria for AEs (CTCAE) and PRO-CTCAE.

RESULTS

Twelve patients were included. Patients had ECOG 0-1; median age was 71 years (51-82). Rectal cancer (n = 11) characteristics included T3 (91%), N1-2 (73%), M0 (73%); 3 had M1a disease suitable for curative-intent treatment. One patient had T2N1M0 ASCC. Prostate cancer risk groups included low (9%), intermediate (45%), and high/very high risk (46%). HypoRT included 45-50 and 67.5 Gy in 25 fx (33%), 46.8-52 and 70.2 Gy in 26 fx (17%), and 44.8-56 and 70 Gy in 28 fx (50%), to the pelvis-anorectum and prostate. Patients with rectal cancer received concurrent capecitabine. Nine (82%) patients with rectal cancer had surgical resection; 1 was R1. The patient with ASCC received concurrent 5-fluorouracil and mitomycin C. Six patients (50%) received androgen suppression. All patients completed treatment successfully but 1 patient with rectal cancer did require hospitalization with treatment break due to GI AEs. Median follow was 60 months (13-103). Oncologic outcomes and AEs are in the table. No patient experienced prostate cancer BCR or ASCC progression. Four of 11 patients with rectal cancer progressed including 3 distant metastases, each amongst initial M1a patients, and 1 local-regrowth in a patient managed non-operatively.

CONCLUSION

HypoRT can effectively be utilized for patients with synchronous prostate and anorectal cancer. Physician assessed AEs compared favorably with prior data, however, further work is needed to understand differences in physician and patient experience. HypoRT may serve as another suitable option in the management of this complex clinical scenario.

Patient-Specific 3D CT Images Reconstruction from 2D KV Images Via Vision Transformer-Based Deep-Learning

PURPOSE/OBJECTIVE(S)

In some proton therapy facilities, patient alignment relies on two 2D orthogonal kV images, taken at fixed, oblique angles, as no 3D on-the-bed-imaging is available. The visibility of the tumor in kV images is limited since the patient's 3D anatomy is projected onto a 2D plane, especially when the tumor is behind a high-density structure such as bone. This can lead to a large patient setup error. A solution to this problem is to reconstruct the 3D CT image from the kV images obtained in the treatment position.

MATERIALS/METHODS

An asymmetric autoencoder-like network built with vision-transformer blocks was developed. The data was collected from a head and neck patient: 2 orthogonal kV images (1024X1024 voxels), 1 3D CT with padding (512X512X512) acquired from the in-room CT-on-rails before kVs were taken and 2 digitally-reconstructed-radiograph (DRR) images (512X512) based on the CT. We resampled kV images every 8 voxels and DRR and CT every 4 voxels, thus formed a dataset consisting of 262,144 samples, in which the images had a dimension of 128 for each direction. The value of each voxel in CT was normalized to range 0-1 with a uniform shift of 1000 and a denominator of 4000. For kV and DRR, we ranked all voxels value in an ascending order and normalized the values of the first 80% voxels to range 0-0.8 and the rest to range 0.8-1, thus yielding a quasi-Gaussian distribution, which was favorable by the deep neural networks. We further cropped kV and DRR images with a self-supervised bitmap based on the voxels' gradients. In training, both kV and DRR were utilized, and the encoder was encouraged to learn the same feature maps for kV images and its corresponding DRR images with mean-absolute-error (MAE) as the similarity loss. Then the decoder would reconstruct the 3D CT image from the feature maps of the kV images with the CT-on-rails as ground-truth (gCT) and MAE as the reconstruction loss. In testing, only independent kV images were used. The full-size synthetic CT (sCT) was achieved by concatenating the sCTs generated by the model according to their spatial information. The image quality of the sCT was evaluated using MAE and per-voxel-absolute-CT-number-difference volume histogram (CDVH). The proposed network was implemented with PyTorch deep learning library and both distributed data parallel (DDP) and automatic mixed precision (AMP) were applied to saving memory and accelerating the training speed. We used the AdamW optimizer with β1 = 0.9 and β2 = 0.999 and a cosine annealing learning rate scheduler with an initial learning of 1e-7 and 20 warm-up epochs.

RESULTS

The model achieved a MAE of <40HU and the CDVH showed that <5% of the voxels had a per-voxel-absolute-CT-number-difference larger than 185HU. The profile of a typical gCT slice and its corresponding sCT slice exhibited a high agreement, indicating the high similarity between the gCT and sCT.

CONCLUSION

A patient-specific vision-transformer-based network was developed and shown to be accurate and efficient to reconstruct 3D CT images from kV images.

Physician and Patient-Reported Outcomes of a Phase III Trial of Ultra-Hypofractionated vs. Moderate Hypofractionated Radiotherapy to the Whole Breast after Breast-Conserving Surgery

PURPOSE/OBJECTIVE(S)

To report a final analysis evaluating physician and patient-reported outcomes of early breast cancer patients receiving moderate hypofractionation or ultra-hypofractionated whole breast radiotherapy (RT).

MATERIALS/METHODS

Between April 4, 2018, and February 11, 2020, patients with localized breast cancer (T1-T3, N0-N1, and M0) managed with breast-conserving surgery (BCS) were enrolled. Patients were randomized to receive whole breast RT with moderate hypofractionation to 40 Gy in 15 fractions (Arm A) or ultra-hypofractionation to 25 Gy in 5 fractions (Arm B). An optional concurrent integrated boost to 48 Gy on Arm A or 30 Gy on Arm B was allowed. Early toxicity (<3 months), late toxicity (> 3 months), quality of life (QOL), cosmesis, Patient-Reported Outcomes version of the Common Terminology Criteria for Adverse Events (PRO-CTCAE), and deterioration of cosmesis were analyzed.

RESULTS

One hundred and seven patients were randomized to moderate hypofractionation (n = 54) or ultra-hypofractionation (n = 53). With a median follow-up of 36 months, no significant differences in patient characteristics were noted between the two arms. There were no patients with a grade ≥3 or higher toxicity. Grade 2 toxicities were 7.4% in Arm A and 7.5% in Arm B, and primarily consisted of radiation dermatitis (6 patients), fibrosis (1 patient) and lymphedema (1 patient). The average Harvard Cosmesis score and overall QoL were similar between arms at all time points, with no patients developing cosmetic deterioration. Patient-reported moderate to severe radiation skin burns were more commonly reported in Arm A (21.05%) vs. Arm B (6.25%) at the end of treatment (EOT) (p = 0.078). At EOT, patients receiving moderate hypofractionation had higher mean toxicity scores in breast tenderness (2.66 vs. 1.5, p = 0.018), skin flaking or peeling (0.63 vs. 0.06, p = 0.035), blistering (0.74 vs. 0.06, p = 0.028), pruritis (2.53 vs. 0.87, p < 0.001), erythema (4.24 vs. 2.0, p <0.001), telangiectasias (1.0 vs. 0.28, p = 0.021). Additionally, patients receiving moderate hypofractionation reported significantly worse changes from baseline at EOT in breast tenderness (-2.25 vs. -.86, p = 0.02), telangiectasia (-0.81 vs. 0.18, p = 0.012), skin discoloration (-4.31 vs. -1.04, p < 0.001), skin flaking or peeling (-.55 vs. 0.04, p = 0.053), blistering (-0.82 vs. -0.07, p = 0.033), and pruritus (-2.27 vs. -.67, p = 0.002). There was a return to baseline in all patient-reported breast domains by 3 months (p >0.05) in both arms.

CONCLUSION

Ultra-hypofractionated whole breast irradiation, consisting of 25 Gy in 5 fractions, provided comparable provider assessed toxicity and cosmetic outcomes to 40 Gy in 15 fractions. At the EOT assessment, ultra-hypofractionation had a better patient reported toxicity profile. Our findings provide further evidence to support daily ultra-hypofractionated whole breast radiotherapy as an appropriate treatment option for early-stage breast cancer.

Oncologic Outcomes of Conventionally Fractionated, Hypofractionated, and Stereotactic Body Spot-Scanned Proton Radiation Therapy for Prostate Cancer: The Mayo Clinic Experience

PURPOSE/OBJECTIVE(S)

Spot/pencil beam scanned proton therapy is a relatively new technology with fundamental differences from double scattered or IMRT. We aimed to report the long-term oncologic outcomes of a contemporary prospective series of patients treated with spot-scanned proton therapy (SSPT).

MATERIALS/METHODS

An IRB-approved prospective registry identified patients with prostate cancer treated with proton therapy between January 2016 and December 2018. Descriptive statistics were calculated for all patients. Clinical, demographic, and treatment characteristics were gathered and analyzed. Kaplan-Meier curves were generated to estimate survival and recurrence rates. Outcomes assessed included 5-year overall survival (OS), 5-year local control (LC), biochemical failure (BF), regional and distant failures, and physician-reported adverse events (AEs). Biochemical failure was defined as rise in PSA ≥ 2.0 ng/mL above nadir PSA. Acute and chronic gastrointestinal (GI) and genitourinary (GU) grade 2+ and grade 3+ baseline-adjusted AEs were assigned using CTCAE v5.0. All failures were re-staged with PET C-11 or PSMA.

RESULTS

With a median follow up of 4.4 years (IQR 3.7 - 5), two hundred and eighty-six prostate cancer patients with a median age of 72 (IQR 67.5 - 77) were treated with spot-scanned proton radiation. The median Gleason grade group was 3 (IQR 2 - 4). The median pre-RT PSA was 6.9 ng/mL (IQR 4.3 - 10.5). Median T-stage was T1c. Nearly 64% of all patients were on androgen deprivation therapy at the time of initiating radiation treatment. The median total radiation dose was 79.2 Gy delivered over 44 fractions, 70 Gy over 28 fractions, and 38 Gy over 5 fractions for CF, HF, and SBRT regimens, respectively. The BF rate for all patients was 8.4%. The 5-year LC rates for CF, HF, and SBRT were 100% (95% CI: 100 - 100), 100% (95% CI: 100 - 100), and 97.3% (95% CI: 92.2 - 100), respectively (p = 0.07). Regional recurrences occurred in 12 (4.2%) patients: 8 (5.6%) treated with CF, 2 (2.1%) with HF, and 2 (4.3%) with SBRT (p = 0.62). Distant metastatic failures occurred in 12 patients (4.2%): 5 (3.5%) treated with CF, 7 (7.4%) with HF, and none with SBRT (0%) (p = 0.052). The 5-year OS for patients treated with CF, HF, and SBRT SSPT were 88.2% (95% CI: 81.8 - 95), 86.2% (95% CI: 77.6 - 95.6), and 97.2% (95% CI: 92 - 100), respectively (p = 0.1). Acute and chronic grade 2+ GI baseline-adjusted AEs occurred in 8 (2.8%) and 51 (17.8%) patients, respectively. Acute and chronic grade 3+ GI baseline-adjusted AEs occurred in 3 (1%) and 4 (1.4%) patients, respectively. Acute and chronic grade 2+ GU-related AEs were observed in 72 (25.2%) and 63 (22%) patients, respectively. Acute and chronic grade 3+ GU toxicity was observed in 3 (1%) and 6 (2.1%) patients, respectively.

CONCLUSION

Spot-scanned proton radiation therapy provides high local control rates and excellent oncologic outcomes across different fractionation schedules with low long-term AE rates.

Complete substitution with modified nucleotides suppresses the early interferon response and increases the potency of self-amplifying RNA

Self-amplifying RNA (saRNA) will revolutionize vaccines and in situ therapeutics by enabling protein expression for longer duration at lower doses. However, a major barrier to saRNA efficacy is the potent early interferon response triggered upon cellular entry, resulting in saRNA degradation and translational inhibition. Substitution of mRNA with modified nucleotides (modNTPs), such as N1-methylpseudouridine (N1mΨ), reduce the interferon response and enhance expression levels. Multiple attempts to use modNTPs in saRNA have been unsuccessful, leading to the conclusion that modNTPs are incompatible with saRNA, thus hindering further development. Here, contrary to the common dogma in the field, we identify multiple modNTPs that when incorporated into saRNA at 100% substitution confer immune evasion and enhance expression potency. Transfection efficiency enhances by roughly an order of magnitude in difficult to transfect cell types compared to unmodified saRNA, and interferon production reduces by >8 fold compared to unmodified saRNA in human peripheral blood mononuclear cells (PBMCs). Furthermore, we demonstrate expression of viral antigens in vitro and observe significant protection against lethal challenge with a mouse-adapted SARS-CoV-2 strain in vivo . A modified saRNA vaccine, at 100-fold lower dose than a modified mRNA vaccine, results in a statistically improved performance to unmodified saRNA and statistically equivalent performance to modified mRNA. This discovery considerably broadens the potential scope of self-amplifying RNA, enabling entry into previously impossible cell types, as well as the potential to apply saRNA technology to non-vaccine modalities such as cell therapy and protein replacement.

Boolean logic in synthetic biology and biomaterials: Towards living materials in mammalian cell therapeutics

BACKGROUND

The intersection of synthetic biology and biomaterials promises to enhance safety and efficacy in novel therapeutics. Both fields increasingly employ Boolean logic, which allows for specific therapeutic outputs (e.g., drug release, peptide synthesis) in response to inputs such as disease markers or bio-orthogonal stimuli. Examples include stimuli-responsive drug delivery devices and logic-gated chimeric antigen receptor (CAR) T cells. In this review, we explore recent manuscripts highlighting the potential of synthetic biology and biomaterials with Boolean logic to create novel and efficacious living therapeutics.

MAIN BODY

Collaborations in synthetic biology and biomaterials have led to significant advancements in drug delivery and cell therapy. Borrowing from synthetic biology, researchers have created Boolean-responsive biomaterials sensitive to multiple inputs including pH, light, enzymes and more to produce functional outputs such as degradation, gel-sol transition and conformational change. Biomaterials also enhance synthetic biology, particularly CAR T and adoptive T cell therapy, by modulating therapeutic immune cells in vivo. Nanoparticles and hydrogels also enable in situ generation of CAR T cells, which promises to drive down production costs and expand access to these therapies to a larger population. Biomaterials are also used to interface with logic-gated CAR T cell therapies, creating controllable cellular therapies that enhance safety and efficacy. Finally, designer cells acting as living therapeutic factories benefit from biomaterials that improve biocompatibility and stability in vivo.

CONCLUSION

By using Boolean logic in both cellular therapy and drug delivery devices, researchers have achieved better safety and efficacy outcomes. While early projects show incredible promise, coordination between these fields is ongoing and growing. We expect that these collaborations will continue to grow and realize the next generation of living biomaterial therapeutics.

Longitudinal Single-Cell Imaging of Engineered Strains with Stimulated Raman Scattering to Characterize Heterogeneity in Fatty Acid Production

Understanding metabolic heterogeneity is critical for optimizing microbial production of valuable chemicals, but requires tools that can quantify metabolites at the single-cell level over time. Here, longitudinal hyperspectral stimulated Raman scattering (SRS) chemical imaging is developed to directly visualize free fatty acids in engineered Escherichia coli over many cell cycles. Compositional analysis is also developed to estimate the chain length and unsaturation of the fatty acids in living cells. This method reveals substantial heterogeneity in fatty acid production among and within colonies that emerges over the course of many generations. Interestingly, the strains display distinct types of production heterogeneity in an enzyme-dependent manner. By pairing time-lapse and SRS imaging, the relationship between growth and production at the single-cell level are examined. The results demonstrate that cell-to-cell production heterogeneity is pervasive and provides a means to link single-cell and population-level production.

Orthogonal inducible control of Cas13 circuits enables programmable RNA regulation in mammalian cells

RNA plays an indispensable role in mammalian cell functions. Cas13, a class of RNA-guided ribonuclease, is a flexible tool for modifying and regulating coding and non-coding RNAs, with enormous potential for creating new cell functions. However, the lack of control over Cas13 activity has limited its cell engineering capability. Here, we present the CRISTAL ( C ontrol of R NA with Inducible S pli T C A s13 Orthologs and Exogenous L igands) platform. CRISTAL is powered by a collection (10 total) of orthogonal split inducible Cas13s that can be turned ON or OFF via small molecules in multiple cell types, providing precise temporal control. Also, we engineered Cas13 logic circuits that can respond to endogenous signaling and exogenous small molecule inputs. Furthermore, the orthogonality, low leakiness, and high dynamic range of our inducible Cas13d and Cas13b enable the design and construction of a robust incoherent feedforward loop, leading to near-perfect and tunable adaptation response. Finally, using our inducible Cas13s, we achieve simultaneous multiplexed control of multiple genes in vitro and in mice. Together, our CRISTAL design represents a powerful platform for precisely regulating RNA dynamics to advance cell engineering and elucidate RNA biology.

The sound of silence: Transgene silencing in mammalian cell engineering

To elucidate principles operating in native biological systems and to develop novel biotechnologies, synthetic biology aims to build and integrate synthetic gene circuits within native transcriptional networks. The utility of synthetic gene circuits for cell engineering relies on the ability to control the expression of all constituent transgene components. Transgene silencing, defined as the loss of expression over time, persists as an obstacle for engineering primary cells and stem cells with transgenic cargos. In this review, we highlight the challenge that transgene silencing poses to the robust engineering of mammalian cells, outline potential molecular mechanisms of silencing, and present approaches for preventing transgene silencing. We conclude with a perspective identifying future research directions for improving the performance of synthetic gene circuits.

Multidimensional control of therapeutic human cell function with synthetic gene circuits

Synthetic gene circuits that precisely control human cell function could expand the capabilities of gene- and cell-based therapies. However, platforms for developing circuits in primary human cells that drive robust functional changes in vivo and have compositions suitable for clinical use are lacking. Here, we developed synthetic zinc finger transcription regulators (synZiFTRs), which are compact and based largely on human-derived proteins. As a proof of principle, we engineered gene switches and circuits that allow precise, user-defined control over therapeutically relevant genes in primary T cells using orthogonal, US Food and Drug Administration-approved small-molecule inducers. Our circuits can instruct T cells to sequentially activate multiple cellular programs such as proliferation and antitumor activity to drive synergistic therapeutic responses. This platform should accelerate the development and clinical translation of synthetic gene circuits in diverse human cell types and contexts.

Small molecule-inducible gene regulatory systems in mammalian cells: progress and design principles

Small molecule-inducible gene circuits are some of the most important tools in biology because they provide a convenient way to exert precise regulation of biological systems. These systems typically are designed to govern gene activation, repression, or disruption at multiple levels, such as through genome modification, transcription, translation, or post-translational regulation of protein activity. Due to their importance, many new systems have been created in the past few years to address different needs or afford orthogonality. They can be broadly characterized based on the inducer used, the mode of regulation, and the effector protein enabling the regulation. Furthermore, each synthetic circuit has varying performance metrics and design considerations. Here, we provide a concise comparison of recently developed tools and recommend standardized metrics for evaluating their performance and potential as biological interrogators or therapeutics.

The future of engineered immune cell therapies

Immune cells are being engineered to recognize and respond to disease states, acting as a "living drug" when transferred into patients. Therapies based on engineered immune cells are now a clinical reality, with multiple engineered T cell therapies approved for treatment of hematologic malignancies. Ongoing preclinical and clinical studies are testing diverse strategies to modify the fate and function of immune cells for applications in cancer, infectious disease, and beyond. Here, we discuss current progress in treating human disease with immune cell therapeutics, emerging strategies for immune cell engineering, and challenges facing the field, with a particular emphasis on the treatment of cancer, where the most effort has been applied to date.

Ganglioside-Functionalized Nanoparticles for Chimeric Antigen Receptor T-Cell Activation at the Immunological Synapse

Chimeric Antigen Receptor (CAR) T cell therapy has proven to be an effective strategy against hematological malignancies but persistence and activity against solid tumors must be further improved. One emerging strategy for enhancing efficacy is based on directing CAR T cells to antigen presenting cells (APCs). Activation of CAR T cells at the immunological synapse (IS) formed between APC and T cell is thought to promote strong, persistent antigen-specific T cell-mediated immune responses but requires integration of CAR ligands into the APC/T-cell interface. Here, we demonstrate that CAR ligand functionalized, lipid-coated, biodegradable polymer nanoparticles (NPs) that contain the ganglioside GM3 (GM3-NPs) bind to CD169 (Siglec-1)-expressing APCs and localize to the cell contact site between APCs and CAR T cells upon initiation of cell conjugates. The CD169+ APC/CAR T-cell interface is characterized by a strong optical colocalization of GM3-NPs and CARs, enrichment of F-actin, and recruitment of ZAP-70, indicative of integration of GM3-NPs into a functional IS. Ligands associated with GM3-NPs localized to the APC/T-cell contact site remain accessible to CARs and result in robust T-cell activation. Overall, this work identifies GM3-NPs as a potential antigen delivery platform for active targeting of CD169 expressing APCs and enhancement of CAR T-cell activation at the NP-containing IS.

Recent progress of gene circuit designs in immune cell therapies

The success of chimeric antigen receptor (CAR) T cell therapy against hematological cancers has convincingly demonstrated the potential of using genetically engineered cells as therapeutic agents. Although much progress has been achieved in cell therapy, more beneficial capabilities have yet to be fully explored. One of the unique advantages afforded by cell therapies is the possibility to implement genetic control circuits, which enables diverse signal sensing and logical processing for optimal response in the complex tumor microenvironment. In this perspective, we will first outline design considerations for cell therapy control circuits that address clinical demands. We will compare and contrast key design features in some of the latest control circuits developments and conclude by discussing potential future directions.

High-performance multiplex drug-gated CAR circuits

Chimeric antigen receptor (CAR) T cells can revolutionize cancer medicine. However, overactivation, lack of tumor-specific surface markers, and antigen escape have hampered CAR T cell development. A multi-antigen targeting CAR system regulated by clinically approved pharmaceutical agents is needed. Here, we present VIPER CARs (versatile protease regulatable CARs), a collection of inducible ON and OFF switch CAR circuits engineered with a viral protease domain. We established their controllability using FDA-approved antiviral protease inhibitors in a xenograft tumor and a cytokine release syndrome mouse model. Furthermore, we benchmarked VIPER CARs against other drug-gated systems and demonstrated best-in-class performance. We showed their orthogonality in vivo using the ON VIPER CAR and OFF lenalidomide-CAR systems. Finally, we engineered several VIPER CAR circuits by combining various CAR technologies. Our multiplexed, drug-gated CAR circuits represent the next progression in CAR design capable of advanced logic and regulation for enhancing the safety of CAR T cell therapy.

Patient-reported outcomes version of the common terminology criteria for adverse events and quality-of-life linear analogue self-assessment in breast cancer patients receiving radiation therapy: single-institution prospective registry

Purpose/objectives

We sought to investigate the impact of patient-reported outcomes version of the common terminology criteria for adverse events (PRO-CTCAE) on overall quality-of-life (QOL) employing linear analogue self-assessment (LASA) in breast cancer (BC) patients undergoing radiation therapy (RT).

Materials/methods

All patients treated with RT for BC with curative intent from 2015 to 2019 at our institution were included. Breast specific PRO-CTCAE and overall QOL LASA questionnaires were administered at baseline, end-of-treatment, 3, 6, 12 months, and then annually. Minimal clinically important difference in overall QOL was a 10-point change in LASA. Hypofractionation was any treatment > 2 Gy per fraction. Mixed models for repeated measures were used to determine the association of PRO-CTCAE and overall QOL LASA.

Results

Three hundred thirty-one (331) patients with a median follow-up of 3.1 years (range 0.4–4.9) were included. Average overall QOL LASA scores were 78.5 at baseline, 79.8 at end-of-treatment, 79.8 at 3 months, 77.1 at 6 months, 79.4 at 12 months, and 79.7 at 24 months. On univariate analysis, patients reporting a grade ≥ 3 PRO-CTCAE had, on average, a 10.4-point reduction in overall LASA QOL (p < 0.0001). On multivariate analysis, not being treated with hypofractionation and higher BMI were predictive for worse overall LASA QOL with a 10-point reduction in LASA for patients reporting a grade ≥ 3 PRO-CTCAE (p < 0.0001).

Conclusions

Patients reporting a grade ≥ 3 PRO-CTCAE experienced statistically significant and clinically meaningful deterioration in overall QOL LASA. Hypofractionation improved QOL while higher BMI predicted for worse QOL. PRO-CTCAE should be integrated into future clinical trials.

Quantitative characterization of recombinase-based digitizer circuits enables predictable amplification of biological signals

Many synthetic gene circuits are restricted to single-use applications or require iterative refinement for incorporation into complex systems. One example is the recombinase-based digitizer circuit, which has been used to improve weak or leaky biological signals. Here we present a workflow to quantitatively define digitizer performance and predict responses to different input signals. Using a combination of signal-to-noise ratio (SNR), area under a receiver operating characteristic curve (AUC), and fold change (FC), we evaluate three small-molecule inducible digitizer designs demonstrating FC up to 508x and SNR up to 3.77 dB. To study their behavior further and improve modularity, we develop a mixed phenotypic/mechanistic model capable of predicting digitizer configurations that amplify a synNotch cell-to-cell communication signal (Δ SNR up to 2.8 dB). We hope the metrics and modeling approaches here will facilitate incorporation of these digitizers into other systems while providing an improved workflow for gene circuit characterization.

Synthetic biology in the clinic: engineering vaccines, diagnostics, and therapeutics

Synthetic biology is a design-driven discipline centered on engineering novel biological functions through the discovery, characterization, and repurposing of molecular parts. Several synthetic biological solutions to critical biomedical problems are on the verge of widespread adoption and demonstrate the burgeoning maturation of the field. Here, we highlight applications of synthetic biology in vaccine development, molecular diagnostics, and cell-based therapeutics, emphasizing technologies approved for clinical use or in active clinical trials. We conclude by drawing attention to recent innovations in synthetic biology that are likely to have a significant impact on future applications in biomedicine.

A mechanistic model of the BLADE platform predicts performance characteristics of 256 different synthetic DNA recombination circuits

Boolean logic and arithmetic through DNA excision (BLADE) is a recently developed platform for implementing inducible and logical control over gene expression in mammalian cells, which has the potential to revolutionise cell engineering for therapeutic applications. This 2-input 2-output platform can implement 256 different logical circuits that exploit the specificity and stability of DNA recombination. Here, we develop the first mechanistic mathematical model of the 2-input BLADE platform based on Cre- and Flp-mediated DNA excision. After calibrating the model on experimental data from two circuits, we demonstrate close agreement between model outputs and data on the other 111 circuits that have so far been experimentally constructed using the 2-input BLADE platform. Model simulations of the remaining 143 circuits that have yet to be tested experimentally predict excellent performance of the 2-input BLADE platform across the range of possible circuits. Circuits from both the tested and untested subsets that perform less well consist of a disproportionally high number of STOP sequences. Model predictions suggested that circuit performance declines with a decrease in recombinase expression and new experimental data was generated that confirms this relationship.

Targeted Chromatinization and Repression of HIV-1 Provirus Transcription with Repurposed CRISPR/Cas9

The major barrier to HIV-1 cure is the persistence of latent provirus, which is not eradicated by antiretroviral therapy. The "shock and kill" approach entails stimulating viral production with latency-reversing agents followed by the killing of cells actively producing the virus by immune clearance. However, this approach does not induce all intact proviruses, leaving a residual reservoir. CRISPR/Cas9 has been utilized to excise integrated Human Immunodeficiency Virus (HIV) DNA from infected cells in an RNA-guided, sequence-specific manner. Here, we seek to epigenetically silence the proviral DNA by introducing nuclease-deficient disabled Cas9 (dCas9) coupled with a transcriptional repressor domain derived from Kruppel-associated box (KRAB). We show that specific guide RNAs (gRNAs) and dCas9-KRAB repress HIV-1 transcription and reactivation of latent HIV-1 provirus. This repression is correlated with chromatin changes, including decreased H3 histone acetylation and increased histone H3 lysine 9 trimethylation, histone marks that are associated with transcriptional repression. dCas9-KRAB-mediated inhibition of HIV-1 transcription suggests that CRISPR can be engineered as a tool for block-and-lock strategies.

Mechanistic modelling of tyrosine recombination reveals key parameters determining the performance of a CAR T cell switching circuit

Inducible genetic switches based on tyrosine recombinase-based DNA excision are a promising platform for the regulation and control of chimeric antigen receptor (CAR) T cell activity in cancer immunotherapy. These switches exploit the increased stability of DNA excision in tyrosine recombinases through an inversion-excision circuit design. Here, the authors develop the first mechanistic mathematical model of switching dynamics in tyrosine recombinases and validate it against experimental data through both global optimisation and statistical approximation approaches. Analysis of this model provides guidelines regarding which system parameters are best suited to experimental tuning in order to establish optimal switch performance in vivo. In particular, they find that the switching response can be made significantly faster by increasing the concentration of the inducer drug 4-OHT and/or by using promoters generating higher expression levels of the FlpO recombinase.

Light-Inducible Recombinases for Bacterial Optogenetics

Optogenetic tools can provide direct and programmable control of gene expression. Light-inducible recombinases, in particular, offer a powerful method for achieving precise spatiotemporal control of DNA modification. However, to-date this technology has been largely limited to eukaryotic systems. Here, we develop optogenetic recombinases for Escherichia coli that activate in response to blue light. Our approach uses a split recombinase coupled with photodimers, where blue light brings the split protein together to form a functional recombinase. We tested both Cre and Flp recombinases, Vivid and Magnet photodimers, and alternative protein split sites in our analysis. The optimal configuration, Opto-Cre-Vvd, exhibits strong blue light-responsive excision and low ambient light sensitivity. For this system we characterize the effect of light intensity and the temporal dynamics of light-induced recombination. These tools expand the microbial optogenetic toolbox, offering the potential for precise control of DNA excision with light-inducible recombinases in bacteria.

High-performance chemical- and light-inducible recombinases in mammalian cells and mice

Site-specific DNA recombinases are important genome engineering tools. Chemical- and light-inducible recombinases, in particular, enable spatiotemporal control of gene expression. However, inducible recombinases are scarce due to the challenge of engineering high performance systems, thus constraining the sophistication of genetic circuits and animal models that can be created. Here we present a library of >20 orthogonal inducible split recombinases that can be activated by small molecules, light and temperature in mammalian cells and mice. Furthermore, we engineer inducible split Cre systems with better performance than existing systems. Using our orthogonal inducible recombinases, we create a genetic switchboard that can independently regulate the expression of 3 different cytokines in the same cell, a tripartite inducible Flp, and a 4-input AND gate. We quantitatively characterize the inducible recombinases for benchmarking their performances, including computation of distinguishability of outputs. This library expands capabilities for multiplexed mammalian gene expression control.

Targeting HIV-1 proviral transcription

Despite the success of antiretroviral therapies, there is no cure for HIV-1 infection due to the establishment of a long-lived latent reservoir that fuels viral rebound upon treatment interruption. 'Shock-and-kill' strategies to diminish the latent reservoir have had modest impact on the reservoir leading to considerations of alternative approaches to target HIV-1 proviruses. This review explores approaches to target HIV-1 transcription as a way to block the provirus expression.

Inducible Gene Switches with Memory in Human T Cells for Cellular Immunotherapy

Cell-based therapies that employ engineered T cells—including those modified to express chimeric antigen receptors (CARs)—to target cancer cells have demonstrated promising responses in clinical trials. However, engineered T cell responses must be regulated to prevent severe side effects such as cytokine storms and off-target responses. Here we present a class of recombinase-based gene circuits that will enable inducible, one-time state switching in adoptive T cell therapy using an FDA-approved drug, creating a generalizable platform that can be used to control when and how strongly a gene is expressed. These circuits exhibit memory such that induced T cells will maintain any changes made even when the drug inducer is removed. This memory feature avoids prolonged drug inducer exposure, thus reducing the complexity and potential side effect associated with the drug inducer. We have utilized these circuits to control the expression of an anti-Her2-CAR, demonstrating the ability of these circuits to regulate CAR expression and T cell activity. We envision this platform can be extended to regulate other genes involved in T cell behavior for applications in various adoptive T cell therapies.

Strength of T cell signaling regulates HIV-1 replication and establishment of latency

A major barrier to curing HIV-1 is the long-lived latent reservoir that supports re-emergence of HIV-1 upon treatment interruption. Targeting this reservoir will require mechanistic insights into the establishment and maintenance of HIV-1 latency. Whether T cell signaling at the time of HIV-1 infection influences productive replication or latency is not fully understood. We used a panel of chimeric antigen receptors (CARs) with different ligand binding affinities to induce a range of signaling strengths to model differential T cell receptor signaling at the time of HIV-1 infection. Stimulation of T cell lines or primary CD4+ T cells expressing chimeric antigen receptors supported HIV-1 infection regardless of affinity for ligand; however, only signaling by the highest affinity receptor facilitated HIV-1 expression. Activation of chimeric antigen receptors that had intermediate and low binding affinities did not support provirus transcription, suggesting that a minimal signal is required for optimal HIV-1 expression. In addition, strong signaling at the time of infection produced a latent population that was readily inducible, whereas latent cells generated in response to weaker signals were not easily reversed. Chromatin immunoprecipitation showed HIV-1 transcription was limited by transcriptional elongation and that robust signaling decreased the presence of negative elongation factor, a pausing factor, by more than 80%. These studies demonstrate that T cell signaling influences HIV-1 infection and the establishment of different subsets of latently infected cells, which may have implications for targeting the HIV-1 reservoir.

Activation of CD4+ T cells facilitates HIV-1 infection; however, whether there are minimal signals required for the establishment of infection, replication, and latency has not been explored. To determine how T cell signaling influences HIV-1 infection and the generation of latently infected cells, we used chimeric antigen receptors to create a tunable model. Stronger signals result in robust HIV-1 expression and an inducible latent population. Minimal signals predispose cells towards latent infections that are refractory to reversal. We discovered that repression of HIV-1 transcription immediately after infection is due to RNA polymerase II pausing and inefficient transcription elongation. These studies demonstrate that signaling events influence the course of HIV-1 infection and have implications for cure strategies. They also provide a mechanistic explanation for why a significant portion of the HIV-1 latent reservoir is not responsive to latency reversing agents which function by modifying chromatin.

Cardiovascular disease-related mortality and factors associated with cardiovascular events in the TREAT Asia HIV Observational Database (TAHOD)

OBJECTIVES

With aging of the HIV-positive population, cardiovascular disease (CVD) increasingly contributes to morbidity and mortality. We investigated CVD-related and other causes of death (CODs) and factors associated with CVD in a multi-country Asian HIV-positive cohort.

METHODS

Patient data from 2003-2017 were obtained from the Therapeutics, Research, Education and AIDS Training in Asia (TREAT Asia) HIV Observational Database (TAHOD). We included patients on antiretroviral therapy (ART) with > 1 day of follow-up. Cumulative incidences were plotted for CVD-related, AIDS-related, non-AIDS-related, and unknown CODs, and any CVD (i.e. fatal and nonfatal). Competing risk regression was used to assess risk factors of any CVD.

RESULTS

Of 8069 patients with a median follow-up of 7.3 years [interquartile range (IQR) 4.4-10.7 years], 378 patients died [incidence rate (IR) 6.2 per 1000 person-years (PY)], and this total included 22 CVD-related deaths (IR 0.36 per 1000 PY). Factors significantly associated with any CVD event (IR 2.2 per 1000 PY) were older age [sub-hazard ratio (sHR) 2.21; 95% confidence interval (CI) 1.36-3.58 for age 41-50 years; sHR 5.52; 95% CI 3.43-8.91 for ≥ 51 years, compared with < 40 years], high blood pressure (sHR 1.62; 95% CI 1.04-2.52), high total cholesterol (sHR 1.89; 95% CI 1.27-2.82), high triglycerides (sHR 1.55; 95% CI 1.02-2.37) and high body mass index (BMI) (sHR 1.66; 95% CI 1.12-2.46). CVD crude IRs were lower in the later ART initiation period and in lower middle- and upper middle-income countries.

CONCLUSIONS

The development of fatal and nonfatal CVD events in our cohort was associated with older age, and treatable risk factors such as high blood pressure, triglycerides, total cholesterol and BMI. Lower CVD event rates in middle-income countries may indicate under-diagnosis of CVD in Asian-Pacific resource-limited settings.

Universal Chimeric Antigen Receptors for Multiplexed and Logical Control of T Cell Responses

T cells expressing chimeric antigen receptors (CARs) are promising cancer therapeutic agents, with the prospect of becoming the ultimate smart cancer therapeutics. To expand the capability of CAR T cells, here, we present a split, universal, and programmable (SUPRA) CAR system that simultaneously encompasses multiple critical "upgrades," such as the ability to switch targets without re-engineering the T cells, finely tune T cell activation strength, and sense and logically respond to multiple antigens. These features are useful to combat relapse, mitigate over-activation, and enhance specificity. We test our SUPRA system against two different tumor models to demonstrate its broad utility and humanize its components to minimize potential immunogenicity concerns. Furthermore, we extend the orthogonal SUPRA CAR system to regulate different T cell subsets independently, demonstrating a dually inducible CAR system. Together, these SUPRA CARs illustrate that multiple advanced logic and control features can be implemented into a single, integrated system.

Engineering a Dual Small Molecule Gated ZAP70 Switch in T Cells

T cells expressing tumor-specific T cell receptors are promising cancer therapeutic agents, but safety control switches are needed to manage potential side effects arising from overactivity. Here, we present the first dual small molecule-gated ZAP70 signaling switch for the regulation of T cell activity. We show that when an analogue-sensitive ZAP70 allele is fused to the engineered ligand binding domain of the estrogen receptor, ER^T2, its activity can be upregulated to an extent by a metabolite of an FDA-approved tamoxifen, 4-hydroxy-tamoxifen, and downregulated by an ATP analogue, 3-MB-PP1. The strength of early T cell signaling can also be modulated by varying the concentrations of activator and inhibitor, and the switch exhibits temporal control on the time scale of minutes. Interestingly, the switch has the ability to control CD69 and calcium levels in T cells but has limited capabilities in the regulation of downstream cytokine release, suggesting further investigation is needed before it can be implemented in adoptive T cell therapy.

Engineering Axl specific CAR and SynNotch receptor for cancer therapy

Axl is a tyrosine kinase receptor that is commonly overexpressed in many cancers. As such, Axl represents an attractive therapeutic target. The transfer of engineered T cell expressing chimeric antigen receptor (CAR) is an exciting cancer therapeutic approach that shows high efficacy against cancers in clinical trials, especially for B cell malignancies. Furthermore, recently developed synthetic Notch (synNotch) receptor has demonstrated potential in enhancing the specificity of CAR T cell therapy and delivering therapeutic payloads to tumors in an antigen-dependent manner. Therefore, a CAR or synNotch against Axl could be a valuable therapeutic reagent against many cancers. Here, we develop a single-chain variable fragment from a humanized monoclonal antibody against Axl. The scFv is attached to CD3ζ, CD28, and 4-1BB signaling domains to generate an anti-Axl CAR. When introduced into human primary T cells, the anti-Axl CAR can lead to cytokine production and cell killing in response to tumor cells expressing Axl. Moreover, an anti-Axl synNotch generated using the same scFv can be activated with Axl expressing tumor cells. Given the fact that Axl is an important cancer therapeutic target, these receptors could be valuable reagents for developing anti-Axl therapies.

Synthetic Biology: Immunotherapy by Design

Cellular immunotherapy holds great promise for the treatment of human disease. Clinical evidence suggests that T cell immunotherapies have the potential to combat cancers that evade traditional immunotherapy. Despite promising results, adverse effects leading to fatalities have left scientists seeking tighter control over these therapies, which is reflected in the growing body of synthetic biology literature focused on developing tightly controlled, context-independent parts. In addition, researchers are adapting these tools for other uses, such as for the treatment of autoimmune disease, HIV infection, and fungal interactions. We review this body of work and devote special attention to approaches that may lend themselves to the development of an "ideal" therapy: one that is safe, efficient, and easy to manufacture. We conclude with a look toward the future of immunotherapy: how synthetic biology can shift the paradigm from the treatment of disease to a focus on wellness and human health as a whole.

Comparison of Kaposi Sarcoma Risk in Human Immunodeficiency Virus-Positive Adults Across 5 Continents: A Multiregional Multicohort Study

BACKGROUND

We compared Kaposi sarcoma (KS) risk in adults who started antiretroviral therapy (ART) across the Asia-Pacific, South Africa, Europe, Latin, and North America.

METHODS

We included cohort data of human immunodeficiency virus (HIV)-positive adults who started ART after 1995 within the framework of 2 large collaborations of observational HIV cohorts. We present incidence rates and adjusted hazard ratios (aHRs).

RESULTS

We included 208140 patients from 57 countries. Over a period of 1066572 person-years, 2046 KS cases were diagnosed. KS incidence rates per 100000 person-years were 52 in the Asia-Pacific and ranged between 180 and 280 in the other regions. KS risk was 5 times higher in South African women (aHR, 4.56; 95% confidence intervals [CI], 2.73-7.62) than in their European counterparts, and 2 times higher in South African men (2.21; 1.34-3.63). In Europe, Latin, and North America KS risk was 6 times higher in men who have sex with men (aHR, 5.95; 95% CI, 5.09-6.96) than in women. Comparing patients with current CD4 cell counts ≥700 cells/µL with those whose counts were <50 cells/µL, the KS risk was halved in South Africa (aHR, 0.53; 95% CI, .17-1.63) but reduced by ≥95% in other regions.

CONCLUSIONS

Despite important ART-related declines in KS incidence, men and women in South Africa and men who have sex with men remain at increased KS risk, likely due to high human herpesvirus 8 coinfection rates. Early ART initiation and maintenance of high CD4 cell counts are essential to further reducing KS incidence worldwide, but additional measures might be needed, especially in Southern Africa.

Smoking and projected cardiovascular risk in an HIV-positive Asian regional cohort

OBJECTIVES

The aim of the study was to assess the prevalence and characteristics associated with current smoking in an Asian HIV-positive cohort, to calculate the predictive risks of cardiovascular disease (CVD), coronary heart disease (CHD) and myocardial infarction (MI), and to identify the impact that simulated interventions may have.

METHODS

Logistic regression analysis was used to distinguish associated current smoking characteristics. Five-year predictive risks of CVD, CHD and MI and the impact of simulated interventions were calculated utilizing the Data Collection on Adverse Effects of Anti-HIV Drugs Study (D:A:D) algorithm.

RESULTS

Smoking status data were collected from 4274 participants and 1496 of these had sufficient data for simulated intervention calculations. Current smoking prevalence in these two groups was similar (23.2% vs. 19.9%, respectively). Characteristics associated with current smoking included age > 50 years compared with 30-39 years [odds ratio (OR) 0.65; 95% confidence interval (CI) 0.51-0.83], HIV exposure through injecting drug use compared with heterosexual exposure (OR 3.03; 95% CI 2.25-4.07), and receiving antiretroviral therapy (ART) at study sites in Singapore, South Korea, Malaysia, Japan and Vietnam in comparison to Thailand (all OR > 2). Women were less likely to smoke than men (OR 0.11; 95% CI 0.08-0.14). In simulated interventions, smoking cessation demonstrated the greatest impact in reducing CVD and CHD risk and closely approximated the impact of switching from abacavir to an alternate antiretroviral in the reduction of 5-year MI risk.

CONCLUSIONS

Multiple interventions could reduce CVD, CHD and MI risk in Asian HIV-positive patients, with smoking cessation potentially being the most influential.

Coordinated regulation of acid resistance in Escherichia coli

Background

Enteric Escherichia coli survives the highly acidic environment of the stomach through multiple acid resistance (AR) mechanisms. The most effective system, AR2, decarboxylates externally-derived glutamate to remove cytoplasmic protons and excrete GABA. The first described system, AR1, does not require an external amino acid. Its mechanism has not been determined. The regulation of the multiple AR systems and their coordination with broader cellular metabolism has not been fully explored.

Results

We utilized a combination of ChIP-Seq and gene expression analysis to experimentally map the regulatory interactions of four TFs: nac, ntrC, ompR, and csiR. Our data identified all previously in vivo confirmed direct interactions and revealed several others previously inferred from gene expression data. Our data demonstrate that nac and csiR directly modulate AR, and leads to a regulatory network model in which all four TFs participate in coordinating acid resistance, glutamate metabolism, and nitrogen metabolism. This model predicts a novel mechanism for AR1 by which the decarboxylation enzymes of AR2 are used with internally derived glutamate. This hypothesis makes several testable predictions that we confirmed experimentally.

Conclusions

Our data suggest that the regulatory network underlying AR is complex and deeply interconnected with the regulation of GABA and glutamate metabolism, nitrogen metabolism. These connections underlie and experimentally validated model of AR1 in which the decarboxylation enzymes of AR2 are used with internally derived glutamate.

Electronic supplementary material

The online version of this article (doi:10.1186/s12918-016-0376-y) contains supplementary material, which is available to authorized users.

Synthetic biology approaches in cancer immunotherapy, genetic network engineering, and genome editing

Investigations into cells and their contents have provided evolving insight into the emergence of complex biological behaviors. Capitalizing on this knowledge, synthetic biology seeks to manipulate the cellular machinery towards novel purposes, extending discoveries from basic science to new applications. While these developments have demonstrated the potential of building with biological parts, the complexity of cells can pose numerous challenges. In this review, we will highlight the broad and vital role that the synthetic biology approach has played in applying fundamental biological discoveries in receptors, genetic circuits, and genome-editing systems towards translation in the fields of immunotherapy, biosensors, disease models and gene therapy. These examples are evidence of the strength of synthetic approaches, while also illustrating considerations that must be addressed when developing systems around living cells.

Rationally Designed MicroRNA-Based Genetic Classifiers Target Specific Neurons in the Brain

Targeting transgene expression to specific cell types in vivo has proven instrumental in characterizing the functional role of defined cell populations. Genetic classifiers, synthetic transgene constructs designed to restrict expression to particular classes of cells, commonly rely on transcriptional promoters to define cellular specificity. However, the large size of many natural promoters complicates their use in viral vectors, an important mode of transgene delivery in the brain and in human gene therapy. Here, we expanded upon an emerging classifier platform, orthogonal to promoter-based strategies, that exploits endogenous microRNA regulation to target gene expression. Such classifiers have been extensively explored in other tissues; however, their use in the nervous system has thus far been limited to targeting gene expression between neurons and supporting cells. Here, we tested the possibility of using combinatory microRNA regulation to specify gene targeting between neuronal subtypes, and successfully targeted inhibitory cells in the neocortex. These classifiers demonstrate the feasibility of designing a new generation of microRNA-based neuron-type- and brain-region-specific gene expression targeting neurotechnologies.

Synthetic biology in cell-based cancer immunotherapy

The adoptive transfer of genetically engineered T cells with cancer-targeting receptors has shown tremendous promise for eradicating tumors in clinical trials. This form of cellular immunotherapy presents a unique opportunity to incorporate advanced systems and synthetic biology approaches to create cancer therapeutics with novel functions. We first review the development of synthetic receptors, switches, and circuits to control the location, duration, and strength of T cell activity against tumors. In addition, we discuss the cellular engineering and genome editing of host cells (or the chassis) to improve the efficacy of cell-based cancer therapeutics, and to reduce the time and cost of manufacturing.

Phase sensitive SPR sensor for wide dynamic range detection

Phase detection has been utilized to enhance the sensitivity of surface plasmon resonance (SPR) sensors for a long time. However, an inherent drawback for phase sensitive SPR sensors are their limited dynamic range, which has greatly hindered wide applications of such sensors. In this Letter, a design combining phase detection and angular interrogation has been proposed to provide an SPR sensor with both high sensitivity and wide dynamic range. As a result, a resolution of 2.2×10^-7 RIU with a dynamic range of over 0.06 RIU has been achieved simultaneously. An added advantage of this design is the flexibility for sensitivity and dynamic range adjustment.

The first case of Silver-Russell syndrome accompanied by linea alba hernia in China

A 10-month-old Chinese boy presented with delayed motor development for seven months. Blood and biochemistry investigations revealed no abnormalities. The physical examination showed poor postnatal growth (below -2 standard deviation from the mean at diagnosis), preservation of the occipitofrontal head circumference with delayed closure of the anterior fontanel, a classical triangular facial phenotype, asymmetry of the lower extremities and other characteristic features that fulfil the diagnostic criteria of Silver-Russell syndrome clinically. As PubMed and web searches revealed no similar findings, we believe that this may be the first case of Silver-Russell syndrome with linea alba hernia and pes varus reported in China, and possibly the world. The genetic deficit responsible for this case is still under investigation.

Microbial maximal specific growth rate as a square-root function of biomass yield and two kinetic parameters

Understanding how growth rates changes under different perturbations is fundamental to many aspect of microbial physiology. In this work, we experimentally showed that maximal specific growth rate is a square-root function of the biomass yield, the substrate turnover number, and the maximum synthesis rate of the substrate transporter under that condition. We used Escherichia coli cultures in lactose minimal medium as a model system by introducing genetic modifications, in vitro evolution, and ethanol stress to the cell. Deletion of crr affected all three parameters in different directions while deletion of ptsG decreased only the biomass yield. Ethanol stress negatively impacted all three parameters, while anaerobicity decreased biomass yield and transporter synthesis rate. In addition, laboratory evolution increased the growth rate in lactose mostly through enhancing the expression rate of the lac operon. Despite all these changes, the growth rate of the perturbed strain was successfully related to the three parameters by the square-root equation. Thus, this square-root relationship provides insight into how growth rate is altered by different physiological parameters.

A hidden square-root boundary between growth rate and biomass yield

Although the theoretical value of biomass yield can be calculated from metabolic network stoichiometry, the growth rate is difficult to predict. Since the rate and yield can vary independently, no simple relationship has been discovered between these two variables. In this work, we analyzed the well-accepted enzyme kinetics and uncovered a hidden boundary for growth rate, which is determined by the square-root of three physiological parameters: biomass yield, the substrate turnover number, and the maximum synthesis rate of the turnover enzyme. Cells cannot grow faster than the square-root of the product of these parameters. This analysis is supported by experimental data and involves essentially no assumptions except (i) the cell is not undergoing a downshift transition, (ii) substrate uptake enzyme activity is proportional to its copy number. This simple boundary (not correlation) has escaped notice for many decades and suggests that the yield calculation does not predict the growth rate, but gives an upper limit for the growth rate. The relationship also explains how growth rate is affected by the yield and sheds lights on strain design for product formation.

Single-cell zeroth-order protein degradation enhances the robustness of synthetic oscillator

In Escherichia coli, protein degradation in synthetic circuits is commonly achieved by the ssrA-tagged degradation system. In this work, we show that the degradation kinetics for the green fluorescent protein fused with the native ssrA tag in each cell exhibits the zeroth-order limit of the Michaelis–Menten kinetics, rather than the commonly assumed first-order. When measured in a population, the wide distribution of protein levels in the cells distorts the true kinetics and results in a first-order protein degradation kinetics as a population average. Using the synthetic gene-metabolic oscillator constructed previously, we demonstrated theoretically that the zeroth-order kinetics significantly enlarges the parameter space for oscillation and thus enhances the robustness of the design under parametric uncertainty.