Differential pre-malignant programs and microenvironment chart distinct paths to malignancy in human colorectal polyps.

Colorectal cancers (CRCs) arise from precursor polyps whose cellular origins, molecular heterogeneity, and immunogenic potential may reveal diagnostic and therapeutic insights when analyzed at high resolution. We present a single-cell transcriptomic and imaging atlas of the two most common human colorectal polyps, conventional adenomas and serrated polyps, and their resulting CRC counterparts. Integrative analysis of 128 datasets from 62 participants reveals adenomas arise from WNT-driven expansion of stem cells, while serrated polyps derive from differentiated cells through gastric metaplasia. Metaplasia-associated damage is coupled to a cytotoxic immune microenvironment preceding hypermutation, driven partly by antigen-presentation differences associated with tumor cell-differentiation status. Microsatellite unstable CRCs contain distinct non-metaplastic regions where tumor cells acquire stem cell properties and cytotoxic immune cells are depleted. Our multi-omic atlas provides insights into malignant progression of colorectal polyps and their microenvironment, serving as a framework for precision surveillance and prevention of CRC.

Oxidation state-specific fluorescent copper sensors reveal oncogene-driven redox changes that regulate labile copper(II) pools.

Copper is an essential metal nutrient for life that often relies on redox cycling between Cu(I) and Cu(II) oxidation states to fulfill its physiological roles, but alterations in cellular redox status can lead to imbalances in copper homeostasis that contribute to cancer and other metalloplasias with metal-dependent disease vulnerabilities. Copper-responsive fluorescent probes offer powerful tools to study labile copper pools, but most of these reagents target Cu(I), with limited methods for monitoring Cu(II) owing to its potent fluorescence quenching properties. Here, we report an activity-based sensing strategy for turn-on, oxidation state-specific detection of Cu(II) through metal-directed acyl imidazole chemistry. Cu(II) binding to a metal and oxidation state-specific receptor that accommodates the harder Lewis acidity of Cu(II) relative to Cu(I) activates the pendant dye for reaction with proximal biological nucleophiles and concomitant metal ion release, thus avoiding fluorescence quenching. Copper-directed acyl imidazole 649 for Cu(II) (CD649.2) provides foundational information on the existence and regulation of labile Cu(II) pools, including identifying divalent metal transporter 1 (DMT1) as a Cu(II) importer, labile Cu(II) increases in response to oxidative stress induced by depleting total glutathione levels, and reciprocal increases in labile Cu(II) accompanied by decreases in labile Cu(I) induced by oncogenic mutations that promote oxidative stress.

Intramolecular London Dispersion Interactions in Single-Molecule Junctions.

This work shows the first example of using intramolecular London dispersion interactions to control molecular geometry and quantum transport in single-molecule junctions. Flexible σ-bonded molecular junctions typically occupy straight-chain geometries due to steric effects. Here, we synthesize a series of thiomethyl-terminated oligo(dimethylsilmethylene)s that bear [CH2-Si(CH3)2]n repeat units, where all backbone dihedral states are sterically equivalent. Scanning tunneling microscopy break-junction (STM-BJ) measurements and theoretical calculations indicate that in the absence of a strong steric bias concerted intramolecular London dispersion interactions staple the carbosilane backbone into coiled conformations that remain intact even as the junction is stretched to its breakpoint. As these kinked conformations are highly resistive to electronic transport, we observe record-high conductance decay values on an experimental junction length basis (ß = 1.86 ± 0.12 Å-1). These studies reveal the potential of using intramolecular London dispersion interactions to design single-molecule electronics.

Comprehensive suppression of single-molecule conductance using destructive σ-interference.

The tunnelling of electrons through molecules (and through any nanoscale insulating and dielectric material 1 ) shows exponential attenuation with increasing length 2 , a length dependence that is reflected in the ability of the electrons to carry an electrical current. It was recently demonstrated3-5 that coherent tunnelling through a molecular junction can also be suppressed by destructive quantum interference 6 , a mechanism that is not length-dependent. For the carbon-based molecules studied previously, cancelling all transmission channels would involve the suppression of contributions to the current from both the π-orbital and σ-orbital systems. Previous reports of destructive interference have demonstrated a decrease in transmission only through the π-channel. Here we report a saturated silicon-based molecule with a functionalized bicyclo[2.2.2]octasilane moiety that exhibits destructive quantum interference in its σ-system. Although molecular silicon typically forms conducting wires 7 , we use a combination of conductance measurements and ab initio calculations to show that destructive σ-interference, achieved here by locking the silicon-silicon bonds into eclipsed conformations within a bicyclic molecular framework, can yield extremely insulating molecules less than a nanometre in length. Our molecules also exhibit an unusually high thermopower (0.97 millivolts per kelvin), which is a further experimental signature of the suppression of all tunnelling paths by destructive interference: calculations indicate that the central bicyclo[2.2.2]octasilane unit is rendered less conductive than the empty space it occupies. The molecular design presented here provides a proof-of-concept for a quantum-interference-based approach to single-molecule insulators.

Installing Quaternary Germanium Centers in Sila-Diamondoid Cores via Skeletal Isomerization.

This manuscript describes skeletal isomerization strategies to install one to four quaternary germanium atoms in the sila-adamantane core, in a cluster analogy to precision germanium doping in silicon-germanium alloys. The first strategy embodies an inorganic variant of single-atom skeletal editing, where we use a sila-Wagner-Meerwein bond shift cascade to exchange a peripheral Ge atom with a core Si atom. We can install up to four Ge atoms at the quaternary diamondoid centers based on controlling the SixGey stoichiometry of our precursor. We find that bridgehead Ge centers can be selectively functionalized over bridgehead Si centers in SiGe adamantanes; we use this chemistry in conjunction with scanning tunneling microscopy break-junction (STM-BJ) measurements to show that Si8Ge2 adamantane wires give a 60% increase in single-molecule conductance compared with Si10 adamantanes. These studies describe the first quantum transport measurements in sila-diamondoid structures, and demonstrate how main-chain Ge doping can be used to increase electronic transmission in sila-diamondoid-based molecular wires.

Associations between Folate and Alcohol Consumption with Colorectal Tumor Ki67 Expression in the Southern Community Cohort Study.

Folate is hypothesized to accelerate cell proliferation in colorectal cancer (CRC) by supporting DNA synthesis, while alcohol is also linked to gastrointestinal epithelial proliferation, despite biological antagonism of folate. We report associations between folate and alcohol consumption with the proliferation marker Ki67 in CRC tumors from the Southern Community Cohort Study. Tumor samples were obtained from formalin-fixed paraffin-embedded tissue blocks. The percentage of cells expressing Ki67 was measured immunohistochemically. Exposures were assessed via questionnaire pre-diagnosis. Associations were assessed via linear regression. In 248 cases (40-78 years), neither dietary folate, folic acid supplements, nor total folate intake were associated with Ki67. Folic acid supplement use was associated with Ki67 in distal/rectal tumors (ß [95% confidence interval]: 7.5 [1.2-13.8], p = .02) but not proximal tumors (-1.4 [-7.1-4.3], p=.62). A positive trend for total folate was observed for distal/rectal tumors (1.6 [0.0-3.3] per 200 µcg, p-trend=.05). Heavy drinking (women: ≥1 drink/day, men: ≥2 drinks/day) was associated with higher Ki67 (6.4 [1.0-11.9], vs. nondrinkers, p=.02), especially for distal/rectal tumors (10.4 [1.6-19.1], p=.02). Negative interaction between alcohol, total folate was observed for distal/rectal tumors (p-interaction=.06). Modest associations between folate, alcohol consumption and distal/rectal tumor Ki67 expression suggest accelerated proliferation, consistent with folate's role in DNA synthesis.

N-3 Long Chain Fatty Acids Supplementation, Fatty Acids Desaturase Activity, and Colorectal Cancer Risk: A Randomized Controlled Trial.

INTRODUCTION: n-3 long-chain polyunsaturated fatty acids (LCPUFA) have anti-inflammatory effects and may reduce colorectal cancer risk. The purpose of this study was to evaluate the effects of n-3 LCPUFA supplementation on markers of rectal cell proliferation and apoptosis and examine how genetic variation in desaturase enzymes might modify this effect. METHODS: We conducted a randomized, double-blind, control six-month trial of 2.5 grams of n-3 LCPUFA per day compared to olive oil. Study participants had a history of colorectal adenomas. Randomization was stratified based on the gene variant rs174535 in the fatty acid desaturase 1 enzyme (FADS1). Our primary outcome was change in markers of rectal epithelial proliferation and apoptosis. RESULTS: A total of 141 subjects were randomized. We found no difference in apoptosis markers between participants randomized to n-3 LCPUFA compared to olive oil (P = 0.41). N-3 LCPUFA supplementation increased cell proliferation in the lower colonic crypt compared to olive oil (P = 0.03) however baseline indexes of proliferation were different between the groups at randomization. We found no evidence that genotype modified the effect. CONCLUSIONS: Our study did not show evidence of a proliferative or pro-apoptotic effect on n-3 LCPUFA supplementation on rectal mucosa regardless of the FADS genotype.ClinicalTrials.gov Identifier: NCT01661764Supplemental data for this article is available online at https://dx.doi.org/10.1080/01635581.2021.1955286.

Site-Selective Functionalization of Sila-Adamantane and Its Ensuing Optical Effects.

The first syntheses of functionalized sila-adamantanes via site-selective reactions are described. Mechanistic inquiry into the isomerization of sila-adamantane revealed new approaches for installing halides at the 2-position of the cluster. Meanwhile, isomerization via Lewis acid catalysts with non-nucleophilic counteranions provided access to sila-adamantane on the gram-scale, enabling us to discover strategies for substituting its 1-, 3-, 5-, and 7-positions with identical or distinct functional groups. Optical absorbance and density functional theory studies show that σ-withdrawing substituents at the 1-position strongly perturb optical absorbance in sila-adamantane, whereas substituents at the exocyclic and 2-position are optically inert. As silicon diamondoids are atomically precise models for silicon nanocrystals, our findings suggest that passivation at tertiary surface sites carries an outsized impact on the optical properties of surface-functionalized Si nanocrystals.

Association between lincRNA expression and overall survival for patients with triple-negative breast cancer.

PURPOSE: Long intergenic non-coding RNAs (lincRNAs) are increasingly recognized as important regulators for pathogenesis and/or prognosis of breast cancer, including triple-negative breast cancer (TNBC) subtype. However, few previous studies used RNA-sequencing (RNA-Seq) technology, and none included an independent replication. METHODS: To systematically evaluate the association between expression of lincRNAs and TNBC survival, we examined lincRNA expression profiles in TNBC tissues using RNA-Seq data for 200 TNBC patients from the Shanghai Breast Cancer Survival Study (SBCSS) and Southern Community Cohort Study (SCCS). RESULTS: Twenty-five lincRNAs were found to be associated with overall survival (P < 0.05 and no significant heterogeneity across studies at Q statistic P > 0.1), and 61 lincRNAs were associated with disease-free survival (DFS). Among these, two lincRNAs (LINC01270 and LINC00449) were significantly associated with both worse overall survival and DFS and were expressed at significantly higher levels in tumor tissues compared with adjacent normal breast tissues (log2[Fold Change] > 0.5 and FDR < 0.05). We further evaluated the potential functions of LINC01270 and LINC00449 using in vitro functional experiments and found that siRNA-mediated knockdown of LINC01270 and LINC00449 expression significantly decreased cell viability, colony formation and cell migration ability in TNBC cells (P < 0.05). CONCLUSIONS: Evidence from observational studies and in vitro experiments indicates that LINC00449 and LINC01270 may be prognostic biomarkers for TNBC.

Single-cluster electronics.

This article reviews the scope of inorganic cluster compounds interrogated in single-molecule break-junction measurements. This body of work lies at the intersection between the fields of inorganic cluster chemistry and single-molecule electronics, where discrete inorganic cluster molecules are used as the active components in molecular electronic circuitry. We explore the breadth of transition metal and main group cluster compounds that have been studied in single-cluster junctions, largely within the context of scanning tunnelling microscopy break-junction (STM-BJ) measurements. Our discussion centers on how the structure and bonding of inorganic cluster compounds give rise to desirable quantum transport effects such as room-temperature current blockade, sequential tunneling, voltage-gated conductance switching, destructive quantum interference, and high thermoelectric currents.

Permethylation Introduces Destructive Quantum Interference in Saturated Silanes.

The single-molecule conductance of silanes is suppressed due to destructive quantum interference in conformations with cisoid dihedral angles along the molecular backbone. Yet, despite the structural similarity, σ-interference effects have not been observed in alkanes. Here we report that the methyl substituents used in silanes are a prerequisite for σ-interference in these systems. Through density functional theory calculations, we find that the destructive interference is not evident to the same extent in nonmethylated silanes. We find the same is true in alkanes as the transmission is significantly suppressed in permethylated cyclic and bicyclic alkanes. Using scanning tunneling microscope break-junction method we determine the single-molecule conductance of functionalized cyclohexane and bicyclo[2.2.2]octane that are found to be higher than that of equivalent permethylated silanes. Rather than the difference between carbon and silicon atoms in the molecular backbones, our calculations reveal that it is primarily the difference between hydrogen and methyl substituents that result in the different electron transport properties of nonmethylated alkanes and permethylated silanes. Chemical substituents play an important role in determining the single-molecule conductance of saturated molecules, and this must be considered when we improve and expand the chemical design of insulating organic molecules.

Modifiable lifestyle factors associated with risk of sessile serrated polyps, conventional adenomas and hyperplastic polyps.

OBJECTIVE: To identify modifiable factors associated with sessile serrated polyps (SSPs) and compare the association of these factors with conventional adenomas (ADs) and hyperplastic polyps (HPs). DESIGN: We used data from the Tennessee Colorectal Polyp Study, a colonoscopy-based case-control study. Included were 214 SSP cases, 1779 AD cases, 560 HP cases and 3851 polyp-free controls. RESULTS: Cigarette smoking was associated with increased risk for all polyps and was stronger for SSPs than for ADs (OR 1.74, 95% CI 1.16 to 2.62, for current vs never, ptrend=0.008). Current regular use of non-steroidal anti-inflammatory drugs was associated with a 40% reduction in SSP risk in comparison with never users (OR 0.68, 95% CI 0.48 to 0.96, ptrend=0.03), similar to the association with AD. Red meat intake was strongly associated with SSP risk (OR 2.59, 95% CI 1.41 to 4.74 for highest vs lowest intake, ptrend<0.001) and the association with SSP was stronger than with AD (ptrend=0.003). Obesity, folate intake, fibre intake and fat intake were not associated with SSP risk after adjustment for other factors. Exercise, alcohol use and calcium intake were not associated with risk for SSPs. CONCLUSIONS: SSPs share some modifiable risk factors for ADs, some of which are more strongly associated with SSPs than ADs. Thus, preventive efforts to reduce risk for ADs may also be applicable to SSPs. Additionally, SSPs have some distinctive risk factors. Future studies should evaluate the preventive strategies for these factors. The findings from this study also contribute to an understanding of the aetiology and biology of SSPs.

A Modular Ionophore Platform for Liver-Directed Copper Supplementation in Cells and Animals.

Copper deficiency is implicated in a variety of genetic, neurological, cardiovascular, and metabolic diseases. Current approaches for addressing copper deficiency rely on generic copper supplementation, which can potentially lead to detrimental off-target metal accumulation in unwanted tissues and subsequently trigger oxidative stress and damage cascades. Here we present a new modular platform for delivering metal ions in a tissue-specific manner and demonstrate liver-targeted copper supplementation as a proof of concept of this strategy. Specifically, we designed and synthesized an N-acetylgalactosamine-functionalized ionophore, Gal-Cu(gtsm), to serve as a copper-carrying "Trojan Horse" that targets liver-localized asialoglycoprotein receptors (ASGPRs) and releases copper only after being taken up by cells, where the reducing intracellular environment triggers copper release from the ionophore. We utilized a combination of bioluminescence imaging and inductively coupled plasma mass spectrometry assays to establish ASGPR-dependent copper accumulation with this reagent in both liver cell culture and mouse models with minimal toxicity. The modular nature of our synthetic approach presages that this platform can be expanded to deliver a broader range of metals to specific cells, tissues, and organs in a more directed manner to treat metal deficiency in disease.

Large Variations in the Single-Molecule Conductance of Cyclic and Bicyclic Silanes.

Linear silanes are efficient molecular wires due to strong σ-conjugation in the transoid conformation; however, the structure-function relationship for the conformational dependence of the single-molecule conductance of silanes remains untested. Here we report the syntheses, electrical measurements, and theoretical characterization of four series of functionalized cyclic and bicyclic silanes including a cyclotetrasilane, a cyclopentasilane, a bicyclo[2.2.1]heptasilane, and a bicyclo[2.2.2]octasilane, which are all extended by linear silicon linkers of varying length. We find an unusual variation of the single-molecule conductance among the four series at each linker length. We determine the relative conductance of the (bi)cyclic silicon structures by using the common length dependence of the four series rather than comparing the conductance at a single length. In contrast with the cyclic π-conjugated molecules, the conductance of σ-conjugated (bi)cyclic silanes is dominated by a single path through the molecule and is controlled by the dihedral angles along this path. This strong sensitivity to molecular conformation dictates the single-molecule conductance of σ-conjugated silanes and allows for systematic control of the conductance through molecular design.

Silane and Germane Molecular Electronics.

This Account provides an overview of our recent efforts to uncover the fundamental charge transport properties of Si-Si and Ge-Ge single bonds and introduce useful functions into group 14 molecular wires. We utilize the tools of chemical synthesis and a scanning tunneling microscopy-based break-junction technique to study the mechanism of charge transport in these molecular systems. We evaluated the fundamental ability of silicon, germanium, and carbon molecular wires to transport charge by comparing conductances within families of well-defined structures, the members of which differ only in the number of Si (or Ge or C) atoms in the wire. For each family, this procedure yielded a length-dependent conductance decay parameter, ß. Comparison of the different ß values demonstrates that Si-Si and Ge-Ge σ bonds are more conductive than the analogous C-C σ bonds. These molecular trends mirror what is seen in the bulk. The conductance decay of Si and Ge-based wires is similar in magnitude to those from π-based molecular wires such as paraphenylenes However, the chemistry of the linkers that attach the molecular wires to the electrodes has a large influence on the resulting ß value. For example, Si- and Ge-based wires of many different lengths connected with a methyl-thiomethyl linker give ß values of 0.36-0.39 Å-1, whereas Si- and Ge-based wires connected with aryl-thiomethyl groups give drastically different ß values for short and long wires. This observation inspired us to study molecular wires that are composed of both π- and σ-orbitals. The sequence and composition of group 14 atoms in the σ chain modulates the electronic coupling between the π end-groups and dictates the molecular conductance. The conductance behavior originates from the coupling between the subunits, which can be understood by considering periodic trends such as bond length, polarizability, and bond polarity. We found that the same periodic trends determine the electric field-induced breakdown properties of individual Si-Si, Ge-Ge, Si-O, Si-C, and C-C bonds. Building from these studies, we have prepared a system that has two different, alternative conductance pathways. In this wire, we can intentionally break a labile, strained silicon-silicon bond and thereby shunt the current through the secondary conduction pathway. This type of in situ bond-rupture provides a new tool to study single molecule reactions that are induced by electric fields. Moreover, these studies provide guidance for designing dielectric materials as well as molecular devices that require stability under high voltage bias. The fundamental studies on the structure/function relationships of the molecular wires have guided the design of new functional systems based on the Si- and Ge-based wires. For example, we exploited the principle of strain-induced Lewis acidity from reaction chemistry to design a single molecule switch that can be controllably switched between two conductive states by varying the distance between the tip and substrate electrodes. We found that the strain intrinsic to the disilaacenaphthene scaffold also creates two state conductance switching. Finally, we demonstrate the first example of a stereoelectronic conductance switch, and we demonstrate that the switching relies crucially on the electronic delocalization in Si-Si and Ge-Ge wire backbones. These studies illustrate the untapped potential in using Si- and Ge-based wires to design and control charge transport at the nanoscale and to allow quantum mechanics to be used as a tool to design ultraminiaturized switches.

Chemiluminescent Probes for Activity-Based Sensing of Formaldehyde Released from Folate Degradation in Living Mice.

Formaldehyde (FA) is a common environmental toxin that is also produced naturally in the body through a wide range of metabolic and epigenetic processes, motivating the development of new technologies to monitor this reactive carbonyl species (RCS) in living systems. Herein, we report a pair of first-generation chemiluminescent probes for selective formaldehyde detection. Caging phenoxy-dioxetane scaffolds bearing different electron-withdrawing groups with a general 2-aza-Cope reactive formaldehyde trigger provides chemiluminescent formaldehyde probes 540 and 700 (CFAP540 and CFAP700) for visible and near-IR detection of FA in living cells and mice, respectively. In particular, CFAP700 is capable of visualizing FA release derived from endogenous folate metabolism, providing a starting point for the use of CFAPs and related chemical tools to probe FA physiology and pathology, as well as for the development of a broader palette of chemiluminescent activity-based sensing (ABS) probes that can be employed from in vitro biochemical to cell to animal models.

Extreme Conductance Suppression in Molecular Siloxanes.

Single-molecule conductance studies have traditionally focused on creating highly conducting molecular wires. However, progress in nanoscale electronics demands insulators just as it needs conductors. Here we describe the single-molecule length-dependent conductance properties of the classic silicon dioxide insulator. We synthesize molecular wires consisting of Si-O repeat units and measure their conductance through the scanning tunneling microscope-based break-junction method. These molecules yield conductance lower than alkanes of the same length and the largest length-dependent conductance decay of any molecular systems measured to date. We calculate single-molecule junction transmission and the complex band structure of the infinite 1D material for siloxane, in comparison with silane and alkane, and show that the large conductance decay is intrinsic to the nature of the Si-O bond. This work highlights the potential for siloxanes to function as molecular insulators in electronics.

Comparison of biomarker expression between proximal and distal colorectal adenomas: The Tennessee-Indiana Adenoma Recurrence Study.

It is unclear if proximal and distal traditional adenomas present with differences in molecular events which contribute to cancer heterogeneity by tumor anatomical subsite. Participants from a colonoscopy-based study (n = 380) were divided into subgroups based on the location of their most advanced adenoma: proximal, distal, or "equivalent both sides." Eight biomarkers in the most advanced adenomas were evaluated by immunohistochemistry (Ki-67, COX-2, TGFßRII, EGFR, ß-catenin, cyclin D1, c-Myc) or TUNEL (apoptosis). After an adjustment for pathological features, there were no significant differences between proximal and distal adenomas for any biomarker. Conversely, expression levels did vary by other features, such as their size, villous component, and synchronousness. Large adenomas had higher expression levels of Ki-67(P < 0.001), TGFßRII (P < 0.0001), c-Myc (P < 0.001), and cyclin D1 (P < 0.001) in comparison to small adenomas, and tubulovillous/villous adenomas also were more likely to have similar higher expression levels in comparison to tubular adenomas. Adenoma location is not a major determinant of the expression of these biomarkers outside of other pathological features. This study suggests similarly important roles of Wnt/ß-catenin and TGF-ß pathways in carcinogenesis in both the proximal and distal colorectum. © 2016 Wiley Periodicals, Inc.

Silver Makes Better Electrical Contacts to Thiol-Terminated Silanes than Gold.

We report that the single-molecule junction conductance of thiol-terminated silanes with Ag electrodes are higher than the conductance of those formed with Au electrodes. These results are in contrast to the trends in the metal work function Φ(Ag)<Φ(Au). As such, a better alignment of the Au Fermi level to the molecular orbital of silane that mediates charge transport would be expected. This conductance trend is reversed when we replace the thiols with amines, highlighting the impact of metal-S covalent and metal-NH2 dative bonds in controlling the molecular conductance. Density functional theory calculations elucidate the crucial role of the chemical linkers in determining the level alignment when molecules are attached to different metal contacts. We also demonstrate that conductance of thiol-terminated silanes with Pt electrodes is lower than the ones formed with Au and Ag electrodes, again in contrast to the trends in the metal work-functions.