COATI: Multimodal Contrastive Pretraining for Representing and Traversing Chemical Space.

Creating a successful small molecule drug is a challenging multiparameter optimization problem in an effectively infinite space of possible molecules. Generative models have emerged as powerful tools for traversing data manifolds composed of images, sounds, and text and offer an opportunity to dramatically improve the drug discovery and design process. To create generative optimization methods that are more useful than brute-force molecular generation and filtering via virtual screening, we propose that four integrated features are necessary: large, quantitative data sets of molecular structure and activity, an invertible vector representation of realistic accessible molecules, smooth and differentiable regressors that quantify uncertainty, and algorithms to simultaneously optimize properties of interest. Over the course of 12 months, Terray Therapeutics has collected a data set of 2 billion quantitative binding measurements of small molecules to therapeutic targets, which directly motivates multiparameter generative optimization of molecules conditioned on these data. To this end, we present contrastive optimization for accelerated therapeutic inference (COATI), a pretrained, multimodal encoder-decoder model of druglike chemical space. COATI is constructed without any human biasing of features, using contrastive learning from text and 3D representations of molecules to allow for downstream use with structural models. We demonstrate that COATI possesses many of the desired properties of universal molecular embedding: fixed-dimension, invertibility, autoencoding, accurate regression, and low computation cost. Finally, we present a novel metadynamics algorithm for generative optimization using a small subset of our proprietary data collected for a model protein, carbonic anhydrase, designing molecules that satisfy the multiparameter optimization task of potency, solubility, and drug likeness. This work sets the stage for fully integrated generative molecular design and optimization for small molecules.

Trigeneration based on the pyrolysis of rural waste in India: Environmental impact, economic feasibility and business model innovation.

Pyrolysis-based waste-to-bioenergy development has the potential to resolve some of the major challenges facing rural communities in India such as poor electrification, household air pollution, and farmland degradation and contamination. Existing understanding and analysis of the economic feasibility and environmental impact of bioenergy deployment in rural areas is limited by parameter uncertainties, and relevant business model innovation following economic evaluation is even scarcer. This paper uses findings from a new field survey of 1200 rural households to estimate the economic feasibility and environmental impact of a pyrolysis-based bioenergy trigeneration development that was designed to tackle these challenges. Based on the survey results, probability distributions were constructed and used to supply input parameters for cost-benefit analysis and life cycle assessment. Monte Carlo simulation was applied to characterise the uncertainties of economic feasibility and environmental impact accounting. It was shown that the global warming potential of the development was 350 kg of CO2-eq per capita per annum. Also, the survey identified a significant mismatch between feedstock prices considered in the literature and prices asked for by the surveyed villagers. The results of the cost-benefit analysis and life cycle assessment were then applied to propose two novel business models inspired by the Business Model Canvas, which had the potential to achieve up to 90 % economic profitability and result in a benefit-cost ratio of 1.35-1.75. This is the first study achieving combined environmental and economic analysis and business model innovation for rural bioenergy production in developing countries.

Mapping the single cell spatial immune landscapes of the melanoma microenvironment.

Melanoma is a highly immunogenic malignancy with an elevated mutational burden, diffuse lymphocytic infiltration, and one of the highest response rates to immune checkpoint inhibitors (ICIs). However, over half of all late-stage patients treated with ICIs will either not respond or develop progressive disease. Spatial imaging technologies are being increasingly used to study the melanoma tumor microenvironment (TME). The goal of such studies is to understand the complex interplay between the stroma, melanoma cells, and immune cell-types as well as their association with treatment response. Investigators seeking a better understanding of the role of cell location within the TME and the importance of spatial expression of biomarkers are increasingly turning to highly multiplexed imaging approaches to more accurately measure immune infiltration as well as to quantify receptor-ligand interactions (such as PD-1 and PD-L1) and cell-cell contacts. CyTOF-IMC (Cytometry by Time of Flight - Imaging Mass Cytometry) has enabled high-dimensional profiling of melanomas, allowing researchers to identify complex cellular subpopulations and immune cell interactions with unprecedented resolution. Other spatial imaging technologies, such as multiplexed immunofluorescence and spatial transcriptomics, have revealed distinct patterns of immune cell infiltration, highlighting the importance of spatial relationships, and their impact in modulating immunotherapy responses. Overall, spatial imaging technologies are just beginning to transform our understanding of melanoma biology, providing new avenues for biomarker discovery and therapeutic development. These technologies hold great promise for advancing personalized medicine to improve patient outcomes in melanoma and other solid malignancies.

Fecal microbiota transplantation plus anti-PD-1 immunotherapy in advanced melanoma: a phase I trial.

Fecal microbiota transplantation (FMT) represents a potential strategy to overcome resistance to immune checkpoint inhibitors in patients with refractory melanoma; however, the role of FMT in first-line treatment settings has not been evaluated. We conducted a multicenter phase I trial combining healthy donor FMT with the PD-1 inhibitors nivolumab or pembrolizumab in 20 previously untreated patients with advanced melanoma. The primary end point was safety. No grade 3 adverse events were reported from FMT alone. Five patients (25%) experienced grade 3 immune-related adverse events from combination therapy. Key secondary end points were objective response rate, changes in gut microbiome composition and systemic immune and metabolomics analyses. The objective response rate was 65% (13 of 20), including four (20%) complete responses. Longitudinal microbiome profiling revealed that all patients engrafted strains from their respective donors; however, the acquired similarity between donor and patient microbiomes only increased over time in responders. Responders experienced an enrichment of immunogenic and a loss of deleterious bacteria following FMT. Avatar mouse models confirmed the role of healthy donor feces in increasing anti-PD-1 efficacy. Our results show that FMT from healthy donors is safe in the first-line setting and warrants further investigation in combination with immune checkpoint inhibitors. ClinicalTrials.gov identifier NCT03772899 .

Deep Learning Approach for the Discovery of Tumor-Targeting Small Organic Ligands from DNA-Encoded Chemical Libraries.

DNA-Encoded Chemical Libraries (DELs) have emerged as efficient and cost-effective ligand discovery tools, which enable the generation of protein-ligand interaction data of unprecedented size. In this article, we present an approach that combines DEL screening and instance-level deep learning modeling to identify tumor-targeting ligands against carbonic anhydrase IX (CAIX), a clinically validated marker of hypoxia and clear cell renal cell carcinoma. We present a new ligand identification and hit-to-lead strategy driven by machine learning models trained on DELs, which expand the scope of DEL-derived chemical motifs. CAIX-screening datasets obtained from three different DELs were used to train machine learning models for generating novel hits, dissimilar to elements present in the original DELs. Out of the 152 novel potential hits that were identified with our approach and screened in an in vitro enzymatic inhibition assay, 70% displayed submicromolar activities (IC50 < 1 µM). To generate lead compounds that are functionalized with anticancer payloads, analogues of top hits were prioritized for synthesis based on the predicted CAIX affinity and synthetic feasibility. Three lead candidates showed accumulation on the surface of CAIX-expressing tumor cells in cellular binding assays. The best compound displayed an in vitro KD of 5.7 nM and selectively targeted tumors in mice bearing human renal cell carcinoma lesions. Our results demonstrate the synergy between DEL and machine learning for the identification of novel hits and for the successful translation of lead candidates for in vivo targeting applications.

Injury outcomes across Canadian trauma systems: a historical cohort study.

PURPOSE: Most North American trauma systems have designated trauma centres (TCs) including level I (ultraspecialized high-volume metropolitan centres), level II (specialized medium-volume urban centres), and/or level III (semirural or rural centres). Trauma system configuration varies across provinces and it is unclear how these differences influence patient distributions and outcomes. We aimed to compare patient case mix, case volumes, and risk-adjusted outcomes of adults with major trauma admitted to designated level I, II, and III TCs across Canadian trauma systems. METHODS: In a national historical cohort study, we extracted data from Canadian provincial trauma registries on major trauma patients treated between 2013 and 2018 in all designated level I, II, or III TCs in British Columbia, Alberta, Quebec, and Nova Scotia; level I and II TCs in New Brunswick; and four TCs in Ontario. We used multilevel generalized linear models to compare mortality and intensive care unit (ICU) admission and competitive risk models for hospital and ICU length of stay (LOS). Ontario could not be included in outcome comparisons because there were no population-based data from this province. RESULTS: The study sample comprised 50,959 patients. Patient distributions in level I and II TCs were similar across provinces but we observed significant differences in case mix and volumes for level III TCs. There was low variation in risk-adjusted mortality and LOS across provinces and TCs but interprovincial and intercentre variation in risk-adjusted ICU admission was high. CONCLUSIONS: Our results suggest that differences in the functional role of TCs according to their designation level across provinces leads to significant variations in the distribution of patients, case volumes, resource use, and clinical outcomes. These results highlight opportunities to improve Canadian trauma care and underline the need for standardized population-based injury data to support national quality improvement efforts.

RéSUMé: OBJECTIF: La plupart des systèmes de traumatologie nord-américains disposent de centres de traumatologie (CT) désignés, y compris de niveau I (centres métropolitains ultraspécialisés à volume élevé), de niveau II (centres urbains spécialisés à volume moyen) et/ou de niveau III (centres semi-ruraux ou ruraux). La configuration des systèmes de traumatologie varie d'une province à l'autre et nous ne savons pas comment ces différences influent sur la répartition de la patientèle et sur les issues. Notre objectif était de comparer le mélange de cas des patient·es, le volume de cas et les issues ajustées en fonction du risque des adultes ayant subi un traumatisme majeur admis·es dans des CT désignés de niveaux I, II et III dans l'ensemble des systèmes de traumatologie canadiens. MéTHODE: Dans une étude de cohorte historique nationale, nous avons extrait des données des registres provinciaux canadiens de traumatologie sur les patient·es ayant subi un traumatisme majeur traité·es entre 2013 et 2018 dans tous les CT désignés de niveau I, II ou III en Colombie-Britannique, en Alberta, au Québec et en Nouvelle-Écosse, les CT de niveau I et II au Nouveau-Brunswick, et dans quatre CT en Ontario. Nous avons utilisé des modèles linéaires généralisés à plusieurs niveaux pour comparer la mortalité, les admissions en unité de soins intensifs (USI) et les modèles de risque compétitif pour la durée du séjour à l'hôpital et à l'USI. L'Ontario n'a pas pu être inclus dans les comparaisons des devenirs parce qu'il n'y avait pas de données démographiques pour cette province. RéSULTATS: L'échantillon de l'étude comptait 50 959 patient·es. La répartition des patient·es dans les CT de niveaux I et II était similaire d'une province à l'autre, mais nous avons observé des différences significatives dans le mélange des cas et les volumes pour les CT de niveau III. Il y avait une faible variation de la mortalité ajustée en fonction du risque et des durées de séjour entre les provinces et les CT, mais la variation interprovinciale et intercentre des admissions à l'USI ajustées en fonction du risque était élevée. CONCLUSION: Nos résultats suggèrent que les différences dans le rôle fonctionnel des CT selon leur niveau de désignation d'une province à l'autre entraînent des variations importantes dans la répartition des patient·es, le nombre de cas, l'utilisation des ressources et les issues cliniques. Ces résultats mettent en évidence les possibilités d'amélioration des soins de traumatologie au Canada et soulignent la nécessité de disposer de données normalisées sur les blessures dans la population pour appuyer les efforts nationaux d'amélioration de la qualité.

Single-cell spatial immune landscapes of primary and metastatic brain tumours.

Single-cell technologies have enabled the characterization of the tumour microenvironment at unprecedented depth and have revealed vast cellular diversity among tumour cells and their niche. Anti-tumour immunity relies on cell-cell relationships within the tumour microenvironment1,2, yet many single-cell studies lack spatial context and rely on dissociated tissues3. Here we applied imaging mass cytometry to characterize the immunological landscape of 139 high-grade glioma and 46 brain metastasis tumours from patients. Single-cell analysis of more than 1.1 million cells across 389 high-dimensional histopathology images enabled the spatial resolution of immune lineages and activation states, revealing differences in immune landscapes between primary tumours and brain metastases from diverse solid cancers. These analyses revealed cellular neighbourhoods associated with survival in patients with glioblastoma, which we leveraged to identify a unique population of myeloperoxidase (MPO)-positive macrophages associated with long-term survival. Our findings provide insight into the biology of primary and metastatic brain tumours, reinforcing the value of integrating spatial resolution to single-cell datasets to dissect the microenvironmental contexture of cancer.

An indium(I) tetramer bound by anionic N-heterocyclic olefins: ambiphilic reactivity, transmetallation and a rare indium-imide.

An organometallic tetrahedron-shaped indium(I) tetramer [(MeIPrCH)In]4 (MeIPrCH = [(MeCNDipp)2CCH]-; Dipp = 2,6-iPr2C6H3) supported by anionic N-heterocyclic olefin (aNHO) ligands is reported. The monomeric unit of this species exhibits both Lewis acidic and basic character at indium, while the steric profile of the aNHO ligand enables isolation of a rare monomeric imide, RInNR'.

Interpretable machine learning to model biomass and waste gasification.

Machine learning has been regarded as a promising method to better model thermochemical processes such as gasification. However, their black box nature can limit how much one can trust and learn from the developed models. Here seven different machine learning methods have been adopted to model the gasification of biomass and waste across a wide range of operating conditions. Gradient boosting regression has been found to outperform the other model types with a coefficient of determination (R2) of 0.90 when averaged across ten key gasification outputs. Global and local model interpretability methods have been used to illuminate the developed black box models. The studied models were most strongly influenced by the feedstock's particle size and the type of gasifying agent employed. By combining global and local interpretability methods, the understanding of black box models has been improved. This allows policy makers and investors to make more educated decisions about gasification process design.

A nuclear cAMP microdomain suppresses tumor growth by Hippo pathway inactivation.

Cyclic AMP (cAMP) signaling is localized to multiple spatially distinct microdomains, but the role of cAMP microdomains in cancer cell biology is poorly understood. Here, we present a tunable genetic system that allows us to activate cAMP signaling in specific microdomains. We uncover a nuclear cAMP microdomain that activates a tumor-suppressive pathway in a broad range of cancers by inhibiting YAP, a key effector protein of the Hippo pathway, inside the nucleus. We show that nuclear cAMP induces a LATS-dependent pathway leading to phosphorylation of nuclear YAP solely at serine 397 and export of YAP from the nucleus with no change in YAP protein stability. Thus, nuclear cAMP inhibition of nuclear YAP is distinct from other known mechanisms of Hippo regulation. Pharmacologic targeting of specific cAMP microdomains remains an untapped therapeutic approach for cancer; thus, drugs directed at the nuclear cAMP microdomain may provide avenues for the treatment of cancer.

Helicobacter pylori serology is associated with worse overall survival in patients with melanoma treated with immune checkpoint inhibitors.

The microbiome is now regarded as one of the hallmarks of cancer and several strategies to modify the gut microbiota to improve immune checkpoint inhibitor (ICI) activity are being evaluated in clinical trials. Preliminary data regarding the upper gastro-intestinal microbiota indicated that Helicobacter pylori seropositivity was associated with a negative prognosis in patients amenable to ICI. In 97 patients with advanced melanoma treated with ICI, we assessed the impact of H. pylori on outcomes and microbiome composition. We performed H. pylori serology and profiled the fecal microbiome with metagenomics sequencing. Among the 97 patients, 22% were H. pylori positive (Pos). H. pylori Pos patients had a significantly shorter overall survival (p = .02) compared to H. pylori negative (Neg) patients. In addition, objective response rate and progression-free survival were decreased in H. pylori Pos patients. Metagenomics sequencing did not reveal any difference in diversity indexes between the H. pylori groups. At the taxa level, Eubacterium ventriosum, Mediterraneibacter (Ruminococcus) torques, and Dorea formicigenerans were increased in the H. pylori Pos group, while Alistipes finegoldii, Hungatella hathewayi and Blautia producta were over-represented in the H. pylori Neg group. In a second independent cohort of patients with NSCLC, diversity indexes were similar in both groups and Bacteroides xylanisolvens was increased in H. pylori Neg patients. Our results demonstrated that the negative impact of H. pylori on outcomes seem to be independent from the fecal microbiome composition. These findings warrant further validation and development of therapeutic strategies to eradicate H. pylori in immuno-oncology arena.

Long-term follow-up and future direction on the management of chronic lymphocytic leukemia/small lymphocytic leukemia.

OBJECTIVE: Chronic lymphocytic leukemia and small lymphocytic lymphoma remain the most prevalent adult leukemia in Western countries. Novel therapeutics have established long-term efficacy and have changed the landscape in patient management. In contrast, novel approaches pose opportunities for patients to be treated for finite durations. In this manuscript, we highlight long-term safety and efficacy data with Bruton's tyrosine kinase inhibitors and combination BCL2 + anti-CD20 therapies. We also offer key considerations for treatment selection and outline ongoing trials which may continue to expand therapeutic options and approaches. DATA SOURCES: An electronic search of the PubMed database was performed to obtain key literature in chronic lymphocytic leukemia and small lymphocytic lymphoma published using the following search terms: chronic lymphocytic leukemia/small lymphocytic lymphoma, Richter syndrome, and histologic transformation. The search results were narrowed by selecting studies in humans published in English. Results were confined to the following article types: Clinical Trial, Phase II; Clinical Trial, Phase III; Clinical Trial, Phase IV; Guideline; Randomized Controlled Trial; Meta-Analysis; Systematic Reviews; and Validation Studies. DATA SUMMARY: Chronic lymphocytic leukemia and small lymphocytic lymphoma are different manifestations of the same disease and are managed in much the same way. Bruton's tyrosine kinase inhibitors have demonstrated long and durable efficacy benefits in patients with newly diagnosed chronic lymphocytic leukemia/small lymphocytic lymphoma and in the relapsed/refractory setting. Despite these benefits, long terms adverse events have posed challenges for patients and have led to treatment discontinuations. Additionally, the use of monotherapy Bruton's tyrosine kinase inhibitor's requires chronic use of the medications leading to added financial implications. BCL2 inhibition with venetoclax in combination with anti-CD20 monoclonal antibodies has offered a novel and finite treatment approach in frontline and relapsed chronic lymphocytic leukemia/small lymphocytic lymphoma. Ongoing clinical trials are in investigating this modality further to enhance durable responses utilizing a combination Bruton's tyrosine kinase inhibitor's and BCL2 inhibitors. CONCLUSION: The treatment armamentarium of chronic lymphocytic leukemia/small lymphocytic lymphoma continues to evolve. Despite the long term, durable responses with Bruton's tyrosine kinase inhibitor's, it is likely that finite treatment durations could become the standard of care as a result of continued, long-term responses.

Spatially mapping the immune landscape of melanoma using imaging mass cytometry.

Melanoma is an immunogenic cancer with a high response rate to immune checkpoint inhibitors (ICIs). It harbors a high mutation burden compared with other cancers and, as a result, has abundant tumor-infiltrating lymphocytes (TILs) within its microenvironment. However, understanding the complex interplay between the stroma, tumor cells, and distinct TIL subsets remains a substantial challenge in immune oncology. To properly study this interplay, quantifying spatial relationships of multiple cell types within the tumor microenvironment is crucial. To address this, we used cytometry time-of-flight (CyTOF) imaging mass cytometry (IMC) to simultaneously quantify the expression of 35 protein markers, characterizing the microenvironment of 5 benign nevi and 67 melanomas. We profiled more than 220,000 individual cells to identify melanoma, lymphocyte subsets, macrophage/monocyte, and stromal cell populations, allowing for in-depth spatial quantification of the melanoma microenvironment. We found that within pretreatment melanomas, the abundance of proliferating antigen-experienced cytotoxic T cells (CD8+CD45RO+Ki67+) and the proximity of antigen-experienced cytotoxic T cells to melanoma cells were associated with positive response to ICIs. Our study highlights the potential of multiplexed single-cell technology to quantify spatial cell-cell interactions within the tumor microenvironment to understand immune therapy responses.

Melanomas with concurrent BRAF non-p.V600 and NF1 loss-of-function mutations are targetable by BRAF/MEK inhibitor combination therapy.

Although combination BRAF/MEK inhibition has produced significant survival benefits for BRAF p.V600 mutant melanomas, targeted therapies approved for BRAF non-p.V600 mutant melanomas remain limited. Through the analysis of 772 cutaneous melanoma exomes, we reveal that BRAF non-p.V600 mutations co-occurs more frequently with NF1 loss, but not with oncogenic NRAS mutations, than expected by chance. We present cell signaling data, which demonstrate that BRAF non-p.V600 mutants can signal as monomers and dimers within an NF1 loss context. Concordantly, BRAF inhibitors that inhibit both monomeric and dimeric BRAF synergize with MEK inhibition to significantly reduce cell viability in vitro and tumor growth in vivo in BRAF non-p.V600 mutant melanomas with co-occurring NF1 loss-of-function mutations. Our data suggest that patients harboring BRAF non-p.V600 mutant melanomas may benefit from current FDA-approved BRAF/MEK inhibitor combination therapy currently reserved for BRAF p.V600 mutant patients.

The clinical significance of adenomatous polyposis coli (APC) and catenin Beta 1 (CTNNB1) genetic aberrations in patients with melanoma.

BACKGROUND: Melanoma-intrinsic activated ß-catenin pathway, the product of the catenin beta 1 (CTNNB1) gene, has been associated with low/absent tumor-infiltrating lymphocytes, accelerated tumor growth, metastases development, and resistance to anti-PD-L1/anti-CTLA-4 agents in mouse melanoma models. Little is known about the association between the adenomatous polyposis coli (APC) and CTNNB1 gene mutations in stage IV melanoma with immunotherapy response and overall survival (OS). METHODS: We examined the prognostic significance of somatic APC/CTNNB1 mutations in the Cancer Genome Atlas Project for Skin Cutaneous Melanoma (TCGA-SKCM) database. We assessed APC/CTNNB1 mutations as predictors of response to immunotherapies in a clinicopathologically annotated metastatic patient cohort from three US melanoma centers. RESULTS: In the TCGA-SKCM patient cohort (n = 434) presence of a somatic APC/CTNNB1 mutation was associated with a worse outcome only in stage IV melanoma (n = 82, median OS of APC/CTNNB1 mutants vs. wild-type was 8.15 vs. 22.8 months; log-rank hazard ratio 4.20, p = 0.011). APC/CTNNB1 mutation did not significantly affect lymphocyte distribution and density. In the 3-melanoma institution cohort, tumor tissues underwent targeted panel sequencing using two standards of care assays. We identified 55 patients with stage IV melanoma and APC/CTNNB1 genetic aberrations (mut) and 169 patients without (wt). At a median follow-up of more than 25 months for both groups, mut compared with wt patients had slightly more frequent (44% vs. 39%) and earlier (66% vs. 45% within six months from original diagnosis of stage IV melanoma) development of brain metastases. Nevertheless, time-to-development of brain metastases was not significantly different between the two groups. Fortunately, mut patients had similar clinical benefits from PD-1 inhibitor-based treatments compared to wt patients (median OS 26.1 months vs. 29.9 months, respectively, log-rank p = 0.23). Less frequent mutations in the NF1, RAC1, and PTEN genes were seen in the mut compared with wt patients from the 3-melanoma institution cohort. Analysis of brain melanoma tumor tissues from a separate craniotomy patient cohort (n = 55) showed that melanoma-specific, activated ß-catenin (i.e., nuclear localization) was infrequent (n = 3, 6%) and not prognostic in established brain metastases. CONCLUSIONS: APC/CTNNB1 mutations are associated with a worse outcome in stage IV melanoma and early brain metastases independent of tumor-infiltrating lymphocyte density. However, PD1 inhibitor-based treatments provide comparable benefits to both mut and wt patients with stage IV melanoma.

Zinc-Mediated Transmetalation as a Route to Anionic N-Heterocyclic Olefin Complexes in the p-Block.

Anionic N-heterocyclic olefins (aNHOs) are suited well for the stabilization of low-coordinate inorganic complexes, due to their steric tunability and strong σ- and π-electron donating abilities. In this study, the new two-coordinate zinc complex (MeIPrCH)2Zn (MeIPrCH = [(MeCNDipp)2C═CH]-, Dipp = 2,6-diisopropylphenyl) is shown to participate in a broad range of metathesis reactions with main group element-based halides and hydrides. In the case of the group 14 halides, Cl2E·dioxane (E = Ge and Sn), transmetalation occurs to form dinuclear propellane-shaped cations, [(MeIPrCHE)2(µ-Cl)]+, while the aNHO-capped phosphine ligand MeIPrCH-PPh2 is obtained when (MeIPrCH)2Zn is combined with ClPPh2. Lastly, ZnH2 elimination drives transmetalation between (MeIPrCH)2Zn and hydroboranes and hydroalumanes, leading to Lewis acidic aNHO-supported -boryl and -alane products.