Development and validation of AI-assisted transcriptomic signatures to personalize adjuvant chemotherapy in patients with pancreatic ductal adenocarcinoma

BACKGROUND

After surgical resection of pancreatic ductal adenocarcinoma (PDAC), patients are predominantly treated with adjuvant chemotherapy, commonly consisting of gemcitabine-based regimens or the modified FOLFIRINOX regimen (mFFX). While mFFX has been shown to be more effective than gemcitabine-based regimens, it is also associated with higher toxicity. Current treatment decisions are based on patient performance status rather than on the molecular characteristics of the tumor. To address this gap, the goal of this study was to develop drug-specific transcriptomic signatures for personalized chemotherapy treatment.

PATIENTS AND METHODS

We used PDAC datasets from preclinical models, encompassing chemotherapy response profiles for the mFFX-regimen components. From them we identified specific gene transcripts associated with chemotherapy response. Three transcriptomic AI-signatures were obtained by combining Independent Component Analysis, Least Absolute Shrinkage and the Selection Operator-Random Forest approach. We integrated a previously developed gemcitabine signature with three newly developed ones. The machine learning strategy employed to enhance these signatures incorporates transcriptomic features from the tumor microenvironment, leading to the development of the Pancreas-View tool ultimately clinically validated in a cohort of 343 patients from the PRODIGE-24/CCTG PA6 trial.

RESULTS

Patients who were predicted to be sensitive to the administered drugs (n=164; 47.8%) had longer disease-free survival (DFS) than the other patients. The median DFS in the mFFX sensitive group treated with mFFX was 50.0 months (stratified HR: 0.31; 95% CI, 0.21-0.44; p<0.001) and 33.7 months (stratified HR: 0.40; 95% CI, 0.17-0.59; p<0.001) in the gemcitabine sensitive group when treated with gemcitabine. Comparatively patients with signature predictions unmatched with the treatments (n=86; 25.1%) or those resistant to all drugs (n=93; 27.1%) had shorter DFS (10.6 and 10.8 months, respectively).

CONCLUSIONS

This study presents a transcriptome-based tool that was developed using preclinical models and machine learning to accurately predict sensitivity to mFFX and gemcitabine.

Cyclic (amino)(barrelene)carbene Ru-complexes: synthesis and reactivity in olefin metathesis

The synthesis of ruthenium-complexes with cyclic (amino)(barrelene)carbenes (namely CABCs) as ligands is reported. Isolated in moderate to good yields, these new complexes showed impressive thermal stability at 110 °C over several days. Good catalytic performances were demonstrated in various ring-closing metathesis (RCM), macrocyclic-RCM, ring-closing enyne metathesis (RCEYM), cross-metathesis (CM), and ring-opening cross metathesis (ROCM) reactions.

Circularly Polarized Luminescence from Cyclic (Alkyl)(Amino) Carbene Derived Propellers

Organic circularly polarized luminescence (CPL)-active molecular emitters featuring dynamic propeller-like luminophores were prepared in one step from cyclic(alkyl)(amino) carbenes (CAACs). These molecules exhibit through-space arene-arene π- delocalization and rapid intramolecular inter-system crossing (ISC) in line with their helical character.

Iridium(I) complexes with bidentate NHC ligands as catalysts for dehydrogenative directed C-H silylation

A series of (NHC)(cod)Ir(I) complexes bearing NHC-carboxylate ligands were efficiently synthesized and fully characterized. Their solid-state structures confirmed the bidentate coordination mode of these LX-type NHC ligands. These unprecedented iridium(I) complexes demonstrated efficient catalytic activities in dehydrogenative directed C-H silylation of arenes, and allowed for excellent ortho-selectivity control with aromatic silylating agents.

Chiral Atropisomeric-NHC Catechodithiolate Ruthenium Complexes for Z-Selective Asymmetric Ring-Opening Cross Metathesis of Exo-Norbornenes

A set of 16 chiral ruthenium complexes containing atropisomerically stable N-Heterocyclic Carbene (NHC) ligands was synthesized from prochiral NHC precursors. After a rapid screening in asymmetric ring-opening-cross metathesis (AROCM), the most effective chiral atrop BIAN-NHC Ru-catalyst (up to 97:3 er) was then converted to a Z-selective catechodithiolate complex. The latter proved to be highly efficient in Z-selective AROCM of exo-norbornenes affording valuable trans-cyclopentanes with excellent Z-selectivity (>98%) and high enantioselectivity (up to 96.5:3.5 er).

Titanium complexes with unsymmetrically substituted imidazolin-2-iminato ligands

The reaction of the unsymmetrical N-heterocyclic carbenes 1-(2,4,6-trimethylphenyl)-3-(adamantyl)imidazolin-2-ylidene (IAdMes, 1a) and 1-(2,6-diisopropylphenyl)-3-(adamantyl)imidazolin-2-ylidene (IAdDipp, 1b) with trimethylsilyl azide furnished the 2-(trimethylsilylimino)imidazolines 2a (Im^AdMesNSiMe₃) and 2b (Im^AdDippNSiMe₃). Desilylation by stirring in methanol gave the corresponding imidazolin-2-imines 3a (Im^AdMesNH) and 3b (Im^AdDippNH). 2a and 2b were treated with [TiCl₄(THF)₂] (THF = tetrahydrofuran) and [CpTiCl₃] (Cp = η⁵-C₅H₅) to form the mono- and bis(imidazolin-2-iminato) titanium(IV) complexes [(Im^AdRN)TiCl₃] (4, R = Mes, Dipp), [Cp(Im^AdRN)TiCl₂] (5, R = Mes, Dipp), and [(Im^AdRN)₂TiCl₂] (6, R = Mes, Dipp). The crystal structures of all compounds except 2b were determined by X-ray diffraction analysis.

Chiral oxazolidines acting as transient hydroxyalkyl-functionalized N-heterocyclic carbenes: an efficient route to air stable copper and gold complexes for asymmetric catalysis

Optically pure oxazolidines were synthesized in nearly quantitative yields from chiral hydroxyalkyl-functionalized imidazolinium salts. Acting as transient chiral diamino N-heterocyclic carbenes (NHCs), these oxazolidines allowed the efficient formation of well-defined copper(i) and gold(i) hydroxyalkyl-NHC complexes, which could be isolated, for the first time, as air stable complexes after silica gel chromatography. Interestingly, X-ray analysis of gold complexes revealed that the hydroxyl-function is not chelated to the metal. Computational studies suggested that both cyclisation to produce oxazolidine and O–H bond elimination to form the transient carbene (prior to coordination) occur through a concerted mechanism. The novel chiral copper-catalysts, as well as oxazolidines alone (copper free), demonstrated excellent performances in asymmetric conjugate addition and allylic alkylation with high regio- and enantio-selectivities (up to 99% ee).

Well-defined chiral Cu(i) and Au(i) hydroxyalkyl NHC complexes were synthesized from oxazolidines. The copper-catalysts and oxazolidines alone (copper free), demonstrated excellent performances in asymmetric conjugate addition and allylic alkylation.

Ruthenium–NHC complex-catalyzed P(iii)-directed C–H borylation of arylphosphines

Bidentate NHC-based ruthenium catalyst for P(III)-directed ortho C–H borylation of arylphosphines.

Cyclic(alkyl)(amino)carbene Ruthenium Complexes for Z-Stereoselective (Asymmetric) Olefin Metathesis

The first Z-stereoselective catechodithiolate ruthenium complexes containing cyclic(alkyl)(amino)carbene ligands are reported. Isolated in nearly quantitative yields or in-situ generated, these catalysts demonstrated remarkable Z selectivity (Z/E ratio up to >98/2)...

Continuous Flow Z-Stereoselective Olefin Metathesis: Development and Applications in the Synthesis of Pheromones and Macrocyclic Odorant Molecules*

The first continuous flow Z-selective olefin metathesis process is reported. Key to realizing this process was the adequate choice of stereoselective catalysts combined with the design of an appropriate continuous reactor setup. The designed continuous process permits various self-, cross- and macro-ring-closing-metathesis reactions, delivering products in high selectivity and short residence times. This technique is exemplified by direct application to the preparation of a range of pheromones and macrocyclic odorant molecules and culminates in a telescoped Z-selective cross-metathesis/ Dieckmann cyclisation sequence to access (Z)-Civetone, incorporating a serial array of continually stirred tank reactors.

Optically Pure C1-Symmetric Cyclic(alkyl)(amino)carbene Ruthenium Complexes for Asymmetric Olefin Metathesis

An expedient access to the first optically pure ruthenium complexes containing C₁-symmetric cyclic (alkyl)(amino)carbene ligands is reported. They demonstrate excellent catalytic performances in asymmetric olefin metathesis with high enantioselectivities (up to 92% ee). Preliminary mechanistic insights provided by density functional theory models highlight the origin of the enantioselectivity.

Expedient synthesis of conjugated triynes via alkyne metathesis

The first synthesis of conjugated triynes by molybdenum-catalysed alkyne metathesis is reported. Strategic to the success of this approach is the utilization of sterically-hindered diynes that allowed for the site-selective alkyne metathesis to produce the desired conjugated triyne products. The steric hindrance of the alkyne moiety was found to be crucial in preventing the formation of diyne byproducts. This novel synthetic strategy was amenable to self- and cross-metathesis providing straightforward access to the corresponding symmetrical and dissymmetrical triynes with high selectivity.

The first synthesis of symmetrical and dissymmetrical conjugated triynes by self- and cross-metathesis was successfully achieved thanks to the use of hindered diynes.

Copper-catalyzed enantioselective conjugate addition of organometallic reagents to challenging Michael acceptors

The copper-catalyzed enantioselective conjugate addition (ECA) of organometallic nucleophiles to electron-deficient alkenes (Michael acceptors) represents an efficient and attractive methodology for providing a wide range of relevant chiral molecules. In order to increase the attractiveness of this useful catalytic transformation, some Michael acceptors bearing challenging electron-deficient functions (i.e., aldehydes, thioesters, acylimidazoles, N-acyloxazolidinones, N-acylpyrrolidinones, amides, N-acylpyrroles) were recently investigated. Remarkably, only a few chiral copper-based catalytic systems have successfully achieved the conjugate addition of different organometallic reagents to these challenging Michael acceptors, with excellent regio- and enantioselectivity. Furthermore, thanks to their easy derivatization, the resulting chiral conjugated products could be converted into various natural products. The aim of this tutorial review is to summarize recent advances accomplished in this stimulating field.

From Prochiral N-Heterocyclic Carbenes to Optically Pure Metal Complexes: New Opportunities in Asymmetric Catalysis

Well-defined optically pure transition metal (TM) complexes bearing C₁- and C₂-symmetric N-heterocyclic carbene (NHC) ligands were prepared from prochiral NHC precursors. As predicted by DFT calculations, our strategy capitalizes on the formation of a metal-carbene bond which induces an axis of chirality. Configurationally stable atropisomers of various NHC-containing TM complexes were isolated by preparative HPLC on a chiral stationary phase in good yields and excellent optical purities (up to 99.5% ee). The carbene transfer from an optically pure Cu complex to a gold or palladium center reveals, for the first time, a full stereoretentivity, supporting the hypothesis of an associative mechanism for the transmetalation. The potential of these new chiral TM complexes was illustrated in asymmetric catalysis with up to 98% ee.