Biology and Clinical Implications of the 19q13 Aggressive Prostate Cancer Susceptibility Locus.

Genome-wide association studies (GWAS) have identified rs11672691 at 19q13 associated with aggressive prostate cancer (PCa). Here, we independently confirmed the finding in a cohort of 2,738 PCa patients and discovered the biological mechanism underlying this association. We found an association of the aggressive PCa-associated allele G of rs11672691 with elevated transcript levels of two biologically plausible candidate genes, PCAT19 and CEACAM21, implicated in PCa cell growth and tumor progression. Mechanistically, rs11672691 resides in an enhancer element and alters the binding site of HOXA2, a novel oncogenic transcription factor with prognostic potential in PCa. Remarkably, CRISPR/Cas9-mediated single-nucleotide editing showed the direct effect of rs11672691 on PCAT19 and CEACAM21 expression and PCa cellular aggressive phenotype. Clinical data demonstrated synergistic effects of rs11672691 genotype and PCAT19/CEACAM21 gene expression on PCa prognosis. These results provide a plausible mechanism for rs11672691 associated with aggressive PCa and thus lay the ground work for translating this finding to the clinic.

Combined CRISPRi and proteomics screening reveal a cohesin-CTCF-bound allele contributing to increased expression of RUVBL1 and prostate cancer progression.

Genome-wide association studies along with expression quantitative trait locus (eQTL) mapping have identified hundreds of single-nucleotide polymorphisms (SNPs) and their target genes in prostate cancer (PCa), yet functional characterization of these risk loci remains challenging. To screen for potential regulatory SNPs, we designed a CRISPRi library containing 9,133 guide RNAs (gRNAs) to cover 2,166 candidate SNP loci implicated in PCa and identified 117 SNPs that could regulate 90 genes for PCa cell growth advantage. Among these, rs60464856 was covered by multiple gRNAs significantly depleted in screening (FDR < 0.05). Pooled SNP association analysis in the PRACTICAL and FinnGen cohorts showed significantly higher PCa risk for the rs60464856 G allele (p value = 1.2 × 10-16 and 3.2 × 10-7, respectively). Subsequent eQTL analysis revealed that the G allele is associated with increased RUVBL1 expression in multiple datasets. Further CRISPRi and xCas9 base editing confirmed that the rs60464856 G allele leads to elevated RUVBL1 expression. Furthermore, SILAC-based proteomic analysis demonstrated allelic binding of cohesin subunits at the rs60464856 region, where the HiC dataset showed consistent chromatin interactions in prostate cell lines. RUVBL1 depletion inhibited PCa cell proliferation and tumor growth in a xenograft mouse model. Gene-set enrichment analysis suggested an association of RUVBL1 expression with cell-cycle-related pathways. Increased expression of RUVBL1 and activation of cell-cycle pathways were correlated with poor PCa survival in TCGA datasets. Our CRISPRi screening prioritized about one hundred regulatory SNPs essential for prostate cell proliferation. In combination with proteomics and functional studies, we characterized the mechanistic role of rs60464856 and RUVBL1 in PCa progression.

Interaction network of human early embryonic transcription factors.

Embryonic genome activation (EGA) occurs during preimplantation development and is characterized by the initiation of de novo transcription from the embryonic genome. Despite its importance, the regulation of EGA and the transcription factors involved in this process are poorly understood. Paired-like homeobox (PRDL) family proteins are implicated as potential transcriptional regulators of EGA, yet the PRDL-mediated gene regulatory networks remain uncharacterized. To investigate the function of PRDL proteins, we are identifying the molecular interactions and the functions of a subset family of the Eutherian Totipotent Cell Homeobox (ETCHbox) proteins, seven PRDL family proteins and six other transcription factors (TFs), all suggested to participate in transcriptional regulation during preimplantation. Using mass spectrometry-based interactomics methods, AP-MS and proximity-dependent biotin labeling, and chromatin immunoprecipitation sequencing we derive the comprehensive regulatory networks of these preimplantation TFs. By these interactomics tools we identify more than a thousand high-confidence interactions for the 21 studied bait proteins with more than 300 interacting proteins. We also establish that TPRX2, currently assigned as pseudogene, is a transcriptional activator.

SNHG15-mediated feedback loop interplays with HNRNPA1/SLC7A11/GPX4 pathway to promote gastric cancer progression.

Dysregulation of long noncoding RNA (lncRNA) expression plays a pivotal role in the initiation and progression of gastric cancer (GC). However, the regulation of lncRNA SNHG15 in GC has not been well studied. Mechanisms for ferroptosis by SNHG15 have not been revealed. Here, we aimed to explore SNHG15-mediated biological functions and underlying molecular mechanisms in GC. The novel SNHG15 was identified by analyzing RNA-sequencing (RNA-seq) data of GC tissues from our cohort and TCGA dataset, and further validated by qRT-PCR in GC cells and tissues. Gain- and loss-of-function assays were performed to examine the role of SNHG15 on GC both in vitro and in vivo. SNHG15 was highly expressed in GC. The enhanced SNHG15 was positively correlated with malignant stage and poor prognosis in GC patients. Gain- and loss-of-function studies showed that SNHG15 was required to affect GC cell growth, migration and invasion both in vitro and in vivo. Mechanistically, the oncogenic transcription factors E2F1 and MYC could bind to the SNHG15 promoter and enhance its expression. Meanwhile, SNHG15 increased E2F1 and MYC mRNA expression by sponging miR-24-3p. Notably, SNHG15 could also enhance the stability of SLC7A11 in the cytoplasm by competitively binding HNRNPA1. In addition, SNHG15 inhibited ferroptosis through an HNRNPA1-dependent regulation of SLC7A11/GPX4 axis. Our results support a novel model in which E2F1- and MYC-activated SNHG15 regulates ferroptosis via an HNRNPA1-dependent modulation of the SLC7A11/GPX4 axis, which serves as the critical effectors in GC progression, and provides a new therapeutic direction in the treatment of GC.

Comprehensive assessment of cellular senescence in the tumor microenvironment.

Cellular senescence (CS), a state of permanent growth arrest, is intertwined with tumorigenesis. Due to the absence of specific markers, characterizing senescence levels and senescence-related phenotypes across cancer types remain unexplored. Here, we defined computational metrics of senescence levels as CS scores to delineate CS landscape across 33 cancer types and 29 normal tissues and explored CS-associated phenotypes by integrating multiplatform data from ~20 000 patients and ~212 000 single-cell profiles. CS scores showed cancer type-specific associations with genomic and immune characteristics and significantly predicted immunotherapy responses and patient prognosis in multiple cancers. Single-cell CS quantification revealed intra-tumor heterogeneity and activated immune microenvironment in senescent prostate cancer. Using machine learning algorithms, we identified three CS genes as potential prognostic predictors in prostate cancer and verified them by immunohistochemical assays in 72 patients. Our study provides a comprehensive framework for evaluating senescence levels and clinical relevance, gaining insights into CS roles in cancer- and senescence-related biomarker discovery.

Oral pimonidazole unveils clinicopathologic and epigenetic features of hypoxic tumour aggressiveness in localized prostate cancer.

BACKGROUND: Tumor hypoxia is associated with prostate cancer (PCa) treatment resistance and poor prognosis. Pimonidazole (PIMO) is an investigational hypoxia probe used in clinical trials. A better understanding of the clinical significance and molecular alterations underpinning PIMO-labeled tumor hypoxia is needed for future clinical application. Here, we investigated the clinical significance and molecular alterations underpinning PIMO-labeled tumor hypoxia in patients with localized PCa, in order to apply PIMO as a prognostic tool and to identify potential biomarkers for future clinical translation. METHODS: A total of 39 patients with localized PCa were recruited and administered oral PIMO before undergoing radical prostatectomy (RadP). Immunohistochemical staining for PIMO was performed on 37 prostatectomy specimens with staining patterns evaluated and clinical association analyzed. Whole genome bisulfite sequencing was performed using laser-capture of microdissected specimen sections comparing PIMO positive and negative tumor areas. A hypoxia related methylation molecular signature was generated by integrating the differentially methylated regions with previously established RNA-seq datasets. RESULTS: Three PIMO staining patterns were distinguished: diffuse, focal, and comedo-like. The comedo-like staining pattern was more commonly associated with adverse pathology. PIMO-defined hypoxia intensity was positively correlated with advanced pathologic stage, tumor invasion, and cribriform and intraductal carcinoma morphology. The generated DNA methylation signature was found to be a robust hypoxia biomarker, which could risk-stratify PCa patients across multiple clinical datasets, as well as be applicable in other cancer types. CONCLUSIONS: Oral PIMO unveiled clinicopathologic features of disease aggressiveness in localized PCa. The generated DNA methylation signature is a novel and robust hypoxia biomarker that has the potential for future clinical translation.

Thermal Reactions of NiAl3O6+ and Al4O6+ with Methane: Reactivity Enhancement by Doping.

Investigation of the reactivity of heteronuclear metal oxide clusters is an important way to uncover the molecular-level mechanisms of the doping effect. Herein, we performed a comparative study on the reactions of CH4 with NiAl3O6+ and Al4O6+ cluster cations at room temperature to understand the role of Ni during the activation and transformation of methane. Mass spectrometric experiments identify that both NiAl3O6+ and Al4O6+ could bring about hydrogen atom abstraction reaction to generate CH3• radical; however, only NiAl3O6+ has the potential to stabilize [CH3] moiety and then transform [CH3] to CH2O. Density functional theory calculations demonstrate that the terminal oxygen radicals (Ot-•) bound to Al act as the reactive sites for the two clusters to activate the first C-H bond. Although the Ni atom cannot directly participate in methane activation, it can manipulate the electronic environment of the surrounding bridging oxygen atoms (Ob) and enable such Ob to function as an electron reservoir to help Ot-• oxidize CH4 to [H-O-CH3]. The facile reduction of Ni3+ to Ni+ also facilitates the subsequent step of activating the second C-H bond by the bridging "lattice oxygen" (Ob2-), finally enabling the oxidation of methane into formaldehyde. The important role of the dopant Ni played in improving the product selectivity of CH2O for methane conversion discovered in this study allows us to have a possible molecule-level understanding of the excellent performance of the catalysts doping with nickel.

Experimental Reactivity of (MoO3)NO- (N = 1-21) Cluster Anions with C1-C4 Alkanes: A Simple Model to Predict the Reactivity with Methane.

Metal oxide clusters with atomic oxygen radical anions are important model systems to study the mechanisms of activating and transforming very stable alkane molecules under ambient conditions. It is extremely challenging to characterize the activation and conversion of methane, the most stable alkane molecule, by metal oxide cluster anions due to the low reactivity of the anionic species. In this study, using a ship-lock type reactor that could be run at relatively high pressure conditions to provide a high number of collisions in ion-molecule reactions, the rate constants of the reactions between (MoO3)NO- (N = 1-21) cluster anions and the light alkanes (C1-C4) were measured under thermal collision conditions. The relationships among the reaction rates of different alkanes were obtained to establish a model to predict the low rate constants with methane from the high rate constants with C2-C4 alkanes. The model was tested by using available experimental results in literature. This study provides a new method to estimate the relatively low reactivity of atomic oxygen radical anions with methane on metal oxide clusters.

Internal iliac artery ligation as a damage control method in hemodynamically unstable pelvic fractures: A systematic review of the literature.

PURPOSE: Internal iliac artery ligation (IIAL) has been used as a damage control procedure to treat hemodynamically unstable pelvic fracture for many years. However, there is ongoing debate regarding the effectiveness and safety of this hemostatic method. Therefore, we performed a systematic literature review to assess the efficacy and safety of IIAL for pelvic fracture hemostasis. METHODS: Three major databases, PubMed, Embase, and Google Scholar, were searched to screen eligible original studies published in English journals. Two reviewers independently read the titles, abstracts, and full texts of all literature. Articles were included if they reported the use and effects of IIAL. RESULTS: A total of 171 articles were initially identified, with 22 fully meeting the inclusion criteria. Among the analyzed cases, up to 66.7% of patients had associated abdominal and pelvic organ injuries, with the urethra being the most frequently injured organ, followed by the bowel. The outcomes of IIAL for achieving hemostasis in pelvic fractures were found to be satisfactory, with an effective rate of 80%. Hemorrhagic shock was the leading cause of death, followed by craniocerebral injury. Notably, no reports of ischemic complications involving the pelvic organs due to IIAL were found. CONCLUSION: IIAL has a good effect in treating hemodynamically unstable pelvic fracture without the risk of pelvic organ ischemia. This procedure should be considered a priority for hemodynamically unstable pelvic fracture patients with abdominal organ injuries.

C-H Activation by Iron-Vanadium Bimetallic Oxide Cluster Anions FeV3 O10 - and FeV5 O15 - : A Comparison with Scandium-Vanadium Oxide Clusters.

Late transition metal-bonded atomic oxygen radicals (LTM-O⋅- ) have been frequently proposed as important active sites to selectively activate and transform inert alkane molecules. However, it is extremely challenging to characterize the LTM-O⋅- -mediated elementary reactions for clarifying the underlying mechanisms limited by the low activity of LTM-O⋅- radicals that is inaccessible by the traditional experimental methods. Herein, benefiting from our newly-designed ship-lock type reactor, the reactivity of iron-vanadium bimetallic oxide cluster anions FeV3 O10 - and FeV5 O15 - featuring with Fe-O⋅- radicals to abstract a hydrogen atom from C2 -C4 alkanes has been experimentally characterized at 298 K, and the rate constants are determined in the orders of magnitude of 10-14 to 10-16  cm3 molecule-1 s-1 , which are four orders of magnitude slower than the values of counterpart ScV3 O10 - and ScV5 O15 - clusters bearing Sc-O⋅- radicals. Theoretical results reveal that the rearrangements of the electronic and geometric structures during the reaction process function to modulate the activity of Fe-O⋅- . This study not only quantitatively characterizes the elementary reactions of LTM-O⋅- radicals with alkanes, but also provides new insights into structure-activity relationship of M-O⋅- radicals.

Superior Reactivity of Molybdenum-Sulfur Cluster Anions Mo5S2- and Mo5S3- toward Dinitrogen.

Inspired by the fact that Mo is a key element in biological nitrogenase, a series of gas-phase MoxSy- cluster anions are prepared and their reactivity toward N2 is investigated by the combination of mass spectrometry, photoelectron imaging spectroscopy, and density functional theory calculations. The Mo5S2- and Mo5S3- cluster anions show remarkable reactivity compared with the anionic species reported previously. The spectroscopic results in conjunction with theoretical analysis reveal that a facile cleavage of N≡N bonds takes place on Mo5S2- and Mo5S3-. The large dissociative adsorption energy of N2 and the favorable entrance channel for initial N2 approaching are proposed as two decisive factors for the superior reactivity of Mo5S2- and Mo5S3-. Besides, the modulation of S ligands on the reactivity of metal centers with N2 is proposed. The highly reactive metal-sulfur species may be obtained by the coordination of two to three sulfur atoms to bare metal clusters so that an appropriate combination of electronic structures and charge distributions can be achieved.

Thermal Methane Conversion to Formaldehyde Mediated by NiAlO3+ in the Gas Phase.

Understanding the active sites and reaction mechanisms of Ni-based catalysts, such as Ni/Al2O3, toward methane is a prerequisite for improving their rational design. Here, the gas-phase reactivity of NiAlO3+ cations toward CH4 is studied using mass spectrometry combined with density functional theory. Similar to our previous study on NiAl2O4+, we find evidence for the formation of both the methyl radical (CH3•) and formaldehyde (CH2O). The first step for methane activation is hydrogen atom abstraction by the terminal oxygen radical Ni(O)2AlO• from methane forming a [Ni(O)2AlOH+, •CH3] complex and leaving the Ni-oxidation state unchanged. The second C-H bond is subsequently activated by the association of a bridged Ni-O2--Al. The oxidation state of the Ni atom is reduced from +3 to +1 during the formation of formaldehyde. Compared to Al2O3+/CH4 and YAlO3+/CH4 systems, the Ni-atom substitution increases the overall reaction rate by roughly an order of magnitude and yields a CH3•/CH2O branching ratio of 0.62/0.38. The present study provides molecular-level insights into the highly efficient gas-phase reaction mechanism contributing to an improved understanding of methane conversion by Ni/Al2O3 catalysts.

High-temperature reactivity of vanadium oxide clusters in methane activation: Vibrational degrees of freedom matter.

Understanding the properties of small particles working under high-temperature conditions at the atomistic scale is imperative for exact control of related processes, but it is quite challenging to achieve experimentally. Herein, benefitting from state-of-the-art mass spectrometry and by using our newly designed high-temperature reactor, the activity of atomically precise particles of negatively charged vanadium oxide clusters toward hydrogen atom abstraction (HAA) from methane, the most stable alkane molecule, has been measured at elevated temperatures up to 873 K. We discovered the positive correlation between the reaction rate and cluster size that larger clusters possessing greater vibrational degrees of freedom can carry more vibrational energies to enhance the HAA reactivity at high temperature, in contrast with the electronic and geometric issues that control the activity at room temperature. This finding opens up a new dimension, vibrational degrees of freedom, for the simulation or design of particle reactions under high-temperature conditions.

Methane activation by vanadium oxide cluster anions (V2O5)NO- (N = 1-18).

The reactivity of vanadium oxide cluster anions (V2O5)NO- (N = 1-18) that feature with vanadium oxyl radicals (V-O⋅-) toward the most stable alkane, methane, at 273 K has been characterized by employing a newly home-made ship-lock type reactor coupled with a time-of-flight mass spectrometer. The rate constants were determined in the orders of magnitude of 10-16-10-18 cm3 molecule-1 s-1, which significantly breaks the detection limit of predecessors that the reactivity of metal-oxyl radicals (Mn+-O⋅-) with rate constants higher than 10-14 cm3 molecule-1 s-1 could usually be measured. The dynamic structural rearrangement of the cluster skeleton has been proposed to account for the size-dependent reactivity of (V2O5)1-5O- clusters, which may also function in tuning the reactivity of large-sized (V2O5)6-18O- clusters. This work provides new insights into the mechanism of Mn+-O⋅--mediated C-H activation of methane at a strictly molecular level and expands the activity landscape of Mn+-O⋅- radicals.

Size-dependent reactivity of rhodium deuteride cluster anions Rh3Dn - (n = 0-3) toward dinitrogen: The prominent role of σ donation.

Nitrogen (N2) fixation is a challenging task for chemists. Adsorption of N2 on transition metal (TM) sites has been identified as a prerequisite for activating the very stable N≡N triple bond in both industrial and biological processes. The importance of π back-donation (filled orbitals of TM → π* orbitals of N2) between metal sites and N2 has been well elucidated while the role of another classic orbital interaction, namely σ donation (σ orbitals of N2 → empty orbitals of TM), remains ambiguous. Herein, the size-dependent reactivity of trinuclear rhodium deuteride cluster anions Rh3Dn - (n = 0-3) toward N2 adsorption in the gas phase was investigated experimentally and theoretically. A reverse relationship that higher electron-donating ability of clusters corresponds to lower N2 adsorption reactivity was experimentally observed, which is uncommon in N2 activation by gas-phase species. Theoretical analysis revealed that the σ donation rather than the π back-donation plays a predominant role in the adsorption complexes Rh3DnN2 - and the enhanced reactivity upon D addition is ascribed to the lowered energy levels of active orbitals in Rh3Dn - as n increases. This study provides the first experimental evidence to declare the important role of σ donation and new clues for the design of reactive metal species in nitrogen fixation.

Pyrolysis of mass-selected (V2O5)NO- (N = 1-6) clusters in a high-temperature linear ion trap reactor.

A high-temperature linear ion trap that can stably run up to 873 K was newly designed and installed into a homemade reflectron time-of-flight mass spectrometer coupled with a laser ablation cluster source and a quadrupole mass filter. The instrument was used to study the pyrolysis behavior of mass-selected (V2O5)NO- (N = 1-6) cluster anions and the dissociation channels were clarified with atomistic precision. Similar to the dissociation behavior of the heated metal oxide cluster cations reported in literature, the desorption of either atomic oxygen atom or molecular O2 prevailed for the (V2O5)NO- clusters with N = 2-5 at 873 K. However, novel dissociation channels involving fragmentation of (V2O5)NO- to small-sized VxOy - anions concurrent with the release of neutral vanadium oxide species were identified for the clusters with N = 3-6. Significant variations in branching ratios for different dissociation channels were observed as a function of cluster size. Kinetic studies indicated that the dissociation rates of (V2O5)NO- monotonically increased with the increase in cluster size. The internal energies carried by the (V2O5)NO- clusters at 873 K as well as the energetics data for dissociation channels have been theoretically calculated to rationalize the experimental observations. The decomposition behavior of vanadium oxide clusters from this study can provide new insights into the pyrolysis mechanism of metal oxide nanoparticles that are widely used in high temperature catalysis.

Improved production of ß-glucan by a T-DNA-based mutant of Aureobasidium pullulans.

To improve ß-1,3-1,6-D-glucan (ß-glucan) production by Aureobasidium pullulans, an Agrobacterium tumefaciens-mediated transformation method was developed to screen a mutant A. pullulans CGMCC 19650. Based on thermal asymmetric-interlaced PCR detection, DNA sequencing, BLAST analysis, and quantitative real-time PCR assay, the T-DNA was identified to be inserted in the coding region of mal31 gene, which encodes a sugar transporter involved in pullulan biosynthesis in the mutant. The maximal biomass and ß-glucan production under batch fermentation were significantly increased by 47.6% and 78.6%, respectively, while pullulan production was decreased by 41.7% in the mutant, as compared to the parental strain A. pullulans CCTCC M 2012259. Analysis of the physiological mechanism of these changes revealed that mal31 gene disruption increased the transcriptional levels of pgm2, ugp, fks1, and kre6 genes; increased the amounts of key enzymes associated with UDPG and ß-glucan biosynthesis; and improved intracellular UDPG contents and energy supply, all of which favored ß-glucan production. However, the T-DNA insertion decreased the transcriptional levels of ags2 genes, and reduced the biosynthetic capability to form pullulan, resulting in the decrease in pullulan production. This study not only provides an effective approach for improved ß-glucan production by A. pullulans, but also presents an accurate and useful gene for metabolic engineering of the producer for efficient polysaccharide production. KEY POINTS: • A mutant A. pullulans CGMCC 19650 was screened by using the ATMT method. • The mal31 gene encoding a sugar transporter was disrupted in the mutant. • ß-Glucan produced by the mutant was significantly improved.

A long hypoxia-inducible factor 3 isoform 2 is a transcription activator that regulates erythropoietin.

Hypoxia-inducible factor (HIF), an αß dimer, is the master regulator of oxygen homeostasis with hundreds of hypoxia-inducible target genes. Three HIF isoforms differing in the oxygen-sensitive α subunit exist in vertebrates. While HIF-1 and HIF-2 are known transcription activators, HIF-3 has been considered a negative regulator of the hypoxia response pathway. However, the human HIF3A mRNA is subject to complex alternative splicing. It was recently shown that the long HIF-3α variants can form αß dimers that possess transactivation capacity. Here, we show that overexpression of the long HIF-3α2 variant induces the expression of a subset of genes, including the erythropoietin (EPO) gene, while simultaneous downregulation of all HIF-3α variants by siRNA targeting a shared HIF3A region leads to downregulation of EPO and additional genes. EPO mRNA and protein levels correlated with HIF3A silencing and HIF-3α2 overexpression. Chromatin immunoprecipitation analyses showed that HIF-3α2 binding associated with canonical hypoxia response elements in the promoter regions of EPO. Luciferase reporter assays showed that the identified HIF-3α2 chromatin-binding regions were sufficient to promote transcription by all three HIF-α isoforms. Based on these data, HIF-3α2 is a transcription activator that directly regulates EPO expression.

Catalytic Co-Conversion of CH4 and CO2 Mediated by Rhodium-Titanium Oxide Anions RhTiO2.

Catalytic co-conversion of methane with carbon dioxide to produce syngas (2 H2 +2 CO) involves complicated elementary steps and almost all the elementary reactions are performed at the same high temperature conditions in practical thermocatalysis. Here, we demonstrate by mass spectrometric experiments that RhTiO2 - promotes the co-conversion of CH4 and CO2 to free 2 H2 +CO and an adsorbed CO (COads ) at room temperature; the only elementary step that requires the input of external energy is desorption of COads from the RhTiO2 CO- to reform RhTiO2 - . This study not only identifies a promising active species for dry (CO2 ) reforming of methane to syngas, but also emphasizes the importance of temperature control over elementary steps in practical catalysis, which may significantly alleviate the carbon deposition originating from the pyrolysis of methane.

Regulating the Structures of Self-Assembled Mechanically Interlocked Moleculecular Constructs via Dianion Precursor Substituent Effects.

Substituent effects play critical roles in both modulating reaction chemistry and supramolecular self-assembly processes. Using substituted terephthalate dianions (p-phthalic acid dianions; PTADAs), the effect of varying the type, number, and position of the substituents was explored in terms of their ability to regulate the inherent anion complexation features of a tetracationic macrocycle, cyclo[2](2,6-di(1H-imidazol-1-yl)pyridine)[2](1,4-dimethylenebenzene) (referred to as the Texas-sized molecular box; 14+), in the form of its tetrakis-PF6- salt in DMSO. Several of the tested substituents, including 2-OH, 2,5-di(OH), 2,5-di(NH2), 2,5-di(Me), 2,5-di(Cl), 2,5-di(Br), and 2,5-di(I), were found to promote pseudorotaxane formation in contrast to what was seen for the parent PTADA system. Other derivatives of PTADA, including those with 2,3-di(OH), 2,6-di(OH), 2,5-di(OMe), 2,3,5,6-tetra(Cl), and 2,3,5,6-tetra(F) substituents, led only to so-called outside binding, where the anion interacts with 14+ on the outside of the macrocyclic cavity. The differing binding modes produced by the choice of PTADA derivative were found to regulate further supramolecular self-assembly when the reaction components included additional metal cations (M). Depending on the specific choice of PTADA derivatives and metal cations (M = Co2+, Ni2+, Zn2+, Cd2+, Gd3+, Nd3+, Eu3+, Sm3+, Tb3+), constructs involving one-dimensional polyrotaxanes, outside-type rotaxanated supramolecular organic frameworks (RSOFs), or two-dimensional metal-organic rotaxane frameworks (MORFs) could be stabilized. The presence and nature of the substituent were found to dictate which specific higher order self-assembled structure was obtained using a given cation. In the specific case of the 2,5-di(OH), 2,5-di(Cl), and 2,5-di(Br) PTADA derivatives and Eu3+, so-called MORFs with distinct fluorescence emission properties could be produced. The present work serves to illustrate how small changes in guest substitution patterns may be used to control structure well beyond the first interaction sphere.