Patent Application
20230348994
The clinical outcome and treatment response of cancer patients is greatly influenced by the host immune response and its interactions with the tumor. Immunotherapy (immune-based therapy) has transformed standard clinical cancer care and shown very promising results, however, thus far its success is limited to a select group of patients and tumor types.
Therefore, studies have focused on identifying gene signatures that can predict the immune contexture of a tumor, and thus the likelihood of a greater treatment response. Although several prognostic immune gene signatures have been identified, their applicability is limited to few specific cancer types.
A 2007 study found that only one-fifth of transcription across the human genome is associated with protein-coding genes, indicating the presence of at least four times more non-coding than coding RNA sequences. RNAs longer than 200 nucleotides that are not translated into functional proteins are known as long non-coding RNAs (lncRNAs).
The human genome contains more than 18,000 lncRNAs and over 51,000 lncRNA transcripts. The resulting lncRNAs are often capped by 7-methyl guanosine (m7G) at their 5′ ends, polyadenylated at their 3′ ends, and spliced similarly to mRNAs.
LncRNAs are involved in numerous biological processes regulating gene expression and post-transcriptional modification and have been implicated in many diseases including cancer.
Several immune-related lncRNA signatures have been identified with prognostic connotations for specific cancer types, including gastric cancer, breast cancer, head and neck cancer, cutaneous melanoma, lung cancer, colorectal cancer, bladder cancer and hepatocellular carcinoma. However, the prognostic value of these lncRNA signatures are likely limited to the tumor type in which they were identified and may not be applicable to patient cohorts of diverse ancestral origin.
Therefore, improved methods are needed to provide increased prognostic capability.
The present disclosure generally relates to the identification and use of immune related lncRNA signatures having prognostic connotations in numerous cancer types, and in patients of diverse ancestral origin.
Disclosed herein are methods to identify immune related lncRNA signatures in tumor tissues.
Disclosed herein are methods of use of immune related lncRNA signatures to predict clinical outcomes of cancer patients.
Further methods comprise development of a treatment protocol based on the predicted clinical outcome.
The present disclosure also relates to the identification of correlations between immune related lncRNA signatures and immune checkpoint molecules.
The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.
Some definitions are provided hereafter. Nevertheless, definitions may be located in the “Embodiments” section below, and the above header “Definitions” does not mean that such disclosures in the “Embodiments” section are not definitions.
As used in this disclosure and the appended claims, the singular forms “a,” “an” and “the” include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to “a component” or “the component” includes two or more components.
“Administration,” or “to administer” means the step of giving (i.e. administering) a pharmaceutical composition or active ingredient to a subject. The pharmaceutical compositions disclosed herein can be administered via a number of appropriate routes.
The words “comprise,” “comprises” and “comprising” are to be interpreted inclusively rather than exclusively. Likewise, the terms “include,” “including,” “containing” and “having” should all be construed to be inclusive, unless such a construction is clearly prohibited from the context. Further in this regard, these terms specify the presence of the stated features but not preclude the presence of additional or further features.
Nevertheless, the compositions and methods disclosed herein may lack any element that is not specifically disclosed herein. Thus, a disclosure of an embodiment using the term “comprising” is:
The term “and/or” used in the context of “X and/or Y” should be interpreted as “X,” or “Y,” or “X and Y.” Similarly, “at least one of X or Y” should be interpreted as “X,” or “Y,” or “X and Y.”
Where used herein, the terms “example” and “such as,” particularly when followed by a listing of terms, are merely exemplary and illustrative and should not be deemed to be exclusive or comprehensive.
“Cancer” is a disease characterized by uncontrolled growth of cells. The embodiments disclosed herein may target any type of cancer that expresses LDHC or a similar molecule.
“LncRNAs” refers to long non-coding RNAs.
“FOR” or the polymerase chain reaction, is a chemical reaction used to amplify DNA sequences.
“Patient” means a human or non-human subject receiving medical or veterinary care.
“Pharmaceutically acceptable” or “therapeutically acceptable” refers to a substance which does not interfere with the effectiveness or the biological activity of the active ingredients and which is not toxic to a patient.
“Pharmaceutically acceptable carrier” is art-recognized, and includes, for example, pharmaceutically acceptable materials, compositions or vehicles, such as a liquid or solid filler, diluent, excipient, solvent, or encapsulating material, involved in carrying or transporting any subject composition from one organ, or portion of the body, to another organ, or portion of the body. Each carrier must be “acceptable” in the sense of being compatible with the other ingredients of a subject composition and not injurious to the patient. In certain embodiments, a pharmaceutically acceptable carrier is non-pyrogenic.
Exemplary materials which can serve as pharmaceutically acceptable carriers include: sugars, such as lactose, glucose and sucrose; starches, such as corn starch and potato starch; cellulose, and its derivatives, such as sodium carboxymethyl cellulose, ethyl cellulose and cellulose acetate; powdered tragacanth; malt; gelatin; talc; excipients, such as cocoa butter and suppository waxes; oils, such as peanut oil, cottonseed oil, sunflower oil, sesame oil, olive oil, corn oil and soybean oil; glycols, such as propylene glycol; polyols, such as glycerin, sorbitol, mannitol and polyethylene glycol; esters, such as ethyl oleate and ethyl laurate; agar; buffering agents, such as magnesium hydroxide and aluminum hydroxide; alginic acid; pyrogen-free water; isotonic saline; Ringer's solution; ethyl alcohol; phosphate buffer solutions; and other non-toxic compatible substances employed in pharmaceutical formulations.
“Pharmaceutical composition” means a formulation comprising an active ingredient. The word “formulation” means that there is at least one additional ingredient (such as, for example and not limited to, an albumin [such as a human serum albumin or a recombinant human albumin] and/or sodium chloride) in the pharmaceutical composition in addition to a botulinum neurotoxin active ingredient. A pharmaceutical composition is therefore a formulation which is suitable for diagnostic, therapeutic or cosmetic administration to a subject, such as a human patient. The pharmaceutical composition can be in a lyophilized or vacuum dried condition, a solution formed after reconstitution of the lyophilized or vacuum dried pharmaceutical composition with saline or water, for example, or as a solution that does not require reconstitution. As stated, a pharmaceutical composition can be liquid, semi-solid, or solid. A pharmaceutical composition can be animal-protein free.
“Therapeutic formulation” means a formulation that can be used to treat and thereby alleviate a disorder or a disease and/or symptom associated thereof.
“Therapeutically effective amount” means the level, amount or concentration of an agent needed to treat a symptom, disease, disorder, or condition without causing significant negative or adverse side effects.
“Treat,” “treating,” or “treatment” means an alleviation or a reduction (which includes some reduction, a significant reduction, a near total reduction, and a total reduction), resolution or prevention (temporarily or permanently) of a symptom, disease, disorder or condition, so as to achieve a desired therapeutic or cosmetic result, such as by healing of injured or damaged tissue, or by altering, changing, enhancing, improving, ameliorating and/or beautifying an existing or perceived disease, disorder or condition.
The terms “tumor” or “tumour” or “cancer” are used interchangeably.
The present disclosure generally relates to the identification and use of immune-related lncRNA signatures that have prognostic connotations in multiple cancer types, and in patients of diverse ancestral origin.
Thus, disclosed embodiments comprise methods of predicting clinical treatment outcomes, for example treatment outcomes in cancer patients.
For example, in some embodiments of the present disclosure, the immune-related lncRNA signature is a 20-ICRlncRNA signature, comprising the top 20 differentially expressed ir-lncRNAs by ICR, that can predict the clinical outcome of cancer patients (
In other embodiments of the present disclosure, the immune-related lncRNA signature is a 20-ICPlncRNA signature, comprising of the top 20 differentially expressed ir-lncRNAs associated with immune checkpoints, that can predict the clinical outcome of cancer patients (
In some embodiments of the present disclosure, the immune-related lncRNA signature is a 3 ir-lncRNA signature, comprising of the overlap of both 20-lncRNA signatures, that can predict the clinical outcome of cancer patients including breast cancer, head and neck cancers, melanoma, uterine cancer, liver cancer, kidney cancer and low-grade glioma brain cancer (
The present disclosure also relates to the identification of a specific combination of 3 immune-related lncRNAs (not the individual naturally occurring lncRNAs) that has translational potential as a prognostic and predictive tool to improve clinical decision making in 7 cancer types.
In some embodiments of the present disclosure, the 3-lncRNA signature performs equally well as (and in UCEC outperforms) the 20-gene ICR signature to predict the clinical outcome of cancer patients with the advantage that the lncRNA molecular signature is significantly less complex, featuring only 3 molecules.
The present disclosure also relates to the identification of ir-lncRNAs that correlate with immune checkpoint molecules which may indicate that these could be predictive of immune checkpoint expression and possibly immune checkpoint therapy response, a type of immunotherapy that block immune checkpoint proteins from binding with partner proteins.
In other embodiments of the present disclosure, the methods of mapping immune-related lncRNAs to a coding-non-coding network are described that can provide insight into the putative molecular mechanisms underlying ir-lncRNA prognostic and predictive value.
Disclosed embodiments comprise a prognostic and predictive molecular test for cancer, in analogy with for example the OncoType DX or MammaPrint micro-array assays for breast cancer.
In some embodiments of the present disclosure, the use of ir-lncRNA signatures can comprise a PCR-based assay to detect specific lncRNA expression.
In other embodiments of the present disclosure, the use of ir-lncRNA signatures can comprise a stand-alone test, as well as “array” tests using, for example a “Q-chip” device to detect ir-lncRNA expression.
In other embodiments of the present disclosure, the use of ir-lncRNA signatures can comprise a combination of any of the above-mentioned embodiments to detect ir-lncRNA expression. In addition, detection of ir-lncRNA expression can also be accomplished by other methods known to one of ordinary skill in the art.
Turning to the Figures,
Disclosed embodiments can further comprise treatment of cancer, for example in patients whose immune related lncRNA signatures suggest the cancer is likely to progress.
It should be understood that various changes and modifications to the presently preferred embodiments described herein will be apparent to those skilled in the art. Such changes and modifications can be made without departing from the spirit and scope of the present subject matter and without diminishing its intended advantages. It is therefore intended that such changes and modifications be covered by the appended claims.
Few immune-related lncRNA signatures have been reported in cancer; however, their biological and clinical relevance and impact on downstream signaling pathways remain largely unexplored. To address this gap, we developed an analysis pipeline that involves the mapping of immune-related lncRNAs to coding-non-coding gene networks, followed by downstream analysis.
The analysis pipeline was first applied to the TOGA breast cancer dataset whereby key findings were validated in other TOGA cancer datasets. We opted to use the TOGA breast cancer dataset as a discovery cohort given its large sample size, detailed clinical annotation, and robust prognostic significance of the ICR gene signature. First, we applied a 2-step process to the TOGA breast cancer dataset by identifying differentially expressed lncRNAs in immune favorable versus unfavorable breast tumors, followed by determining their proximal coding genes and their likely downstream biological effects through pathways and correlation analyses (
TOGA breast tumor samples were classified into 3 subgroups based on the 20-gene ICR signature, and differentially expressed lncRNAs between ICR low (immune unfavorable) and ICR high (immune favorable) tumors were identified and labeled as immune related lncRNAs (ir-lncRNAs).
Out of a total of 12,727 lncRNAs, we identified 2988 to be differentially expressed (FDR p<0.05) of which 1284 were up- and 1704 were down-regulated in ICR high tumors (
Next, we applied the RWR global propagation network algorithm to map the 2988 ir-lncRNAs to the CNC network and computed propagation scores to identify protein-coding genes within the network that are most likely influenced by the ir-lncRNAs. Based on the propagation scores, a ranked list of 127 unique protein-coding genes with walkscores 0.01 was compiled (Supp) Table 2).
We then performed limma analysis of these 127 protein-coding genes and could confirm that 37 and 40 were significantly up- and downregulated (FDR p<0.05) respectively (
To gain insight into the putative downstream biological roles of the differentially expressed ir-lncRNAs, we explored enriched pathways, diseases and functions associated with the 127 protein-coding genes. Pathway enrichment analysis revealed that pathways involved in ‘Electron Transport Chain (OXPHOS system in mitochondria)’, ‘Respiratory electron transport’, ‘Oxidative phosphorylation’, ‘Complex I biogenesis’ and ‘Formation of ATP by chemiosmotic coupling’ were the most significantly enriched (p<0.05).
The first three pathways were mainly influenced by the differential expression of MT-ND1, MT-ND2, MT-CYB, NDUFB4, COX411, MT-ATP8 and MT-ATP6 genes (
In addition to its prognostic value, the ICR classifier serves as a predictor of response to immune checkpoint blockade. Furthermore, several lncRNAs have been found to be involved in the regulation of the immune checkpoint expression. Hence, we further explored the correlation of the differentially expressed ir-lncRNAs with immune checkpoints in the TCGA-BRCA cohort using Spearman correlation analysis (
Overall, similar correlation patterns were observed between individual ir-lncRNAs and immune checkpoints. The strongest correlating immune checkpoints included CD40, IDO1, ICOS, CTLA4 and LAG3, whereas ADORA2A, VTCN1, CEACAM1 and TNFRSF14 showed the weakest correlations. Notably, CD276 (B7-H3) was the only immune checkpoint that was negatively correlated with ir-lncRNA expression.
Next, we investigated the prognostic value of two ir-lncRNA signatures in breast cancer, the first consisting of the top 20 differentially expressed ir-lncRNAs by ICR (20-ICRlncRNA) and the second of the top 20 differentially expressed ir-lncRNAs associated with immune checkpoints (20-ICPlncRNA). Both ir-lncRNA signatures conferred a significant survival benefit (20-ICRlncRNA [HR=0.2, p<0.01]; 20-ICPlncRNA [HR=0.304, p=0.0204]), with the 20-ICRlncRNA signature even outperforming the ICR score (HR=0.257, p=0.0163) (
Interestingly, the two ir-lncRNA signatures shared 3 common ir-lncRNAs (PCED1B-AS1, RP11-291B21.2 and AC092580.4,
Given the prognostic connotation of the ir-lncRNA signatures in breast tumors, we sought to assess its clinical value across different tumor types in comparison with the ICR classifier. For this purpose, we included TOGA datasets of 18 cancer types for which both gene and lncRNA expression data are available as well as one small breast cancer dataset from Qatar. Forest plot results (
Similarly, we assessed the prognostic value of the 3 ir-lncRNA signature across 18 tumor types (
indicates data missing or illegible when filed
An 18 year old patient is evaluated for cancer prognosis. After identification of at least one ir-lncRNA signature associated with cancer progression, the a treatment protocol including radiation therapy is prescribed.
An 66 year old patient is evaluated for cancer prognosis. After identification of at least one ir-lncRNA signature associated with cancer progression, the a treatment protocol including immunotherapy is prescribed.
An 54 year old patient is evaluated for cancer prognosis. After identification of at least one ir-lncRNA signature associated with cancer progression, the a treatment protocol including chemotherapy is prescribed.
Embodiment 1—A method for predicting clinical outcome in cancer, the method comprising of identification of at least one ir-lncRNA signature, wherein said at least one signature is associated with cancer progression.
Embodiment 2—The method of embodiment 1, wherein the ir-lncRNA signature comprises three lncRNAs.
Embodiment 3—The method of embodiment 1, wherein the ir-lncRNA signature comprises the top 20 differentially expressed ir-lncRNAs in ICR high versus ICR low breast tumors
Embodiment 4—The method of embodiment 1, wherein the ir-lncRNA signature comprises the top 20 ir-lncRNAs that are positively correlated with immune checkpoint expression.
Embodiment 5—The method of embodiment 1, wherein the cancer comprises breast invasive carcinoma, head and neck squamous cell carcinoma, skin cutaneous melanoma, uterine corpus endometrial carcinoma, liver hepatocellular carcinoma, cervical squamous cell carcinoma and endocervical adenocarcinoma, kidney renal papillary cell carcinoma, kidney renal clear cell carcinoma, or low grade glioma.
Embodiment 6—The method of embodiment 5, wherein the cancer comprises one or any combination of the above-mentioned cancers.
Embodiment 7—A method of correlating immune checkpoint expression with one ir-lncRNA signature or a combination of ir-lncRNA signatures, the method comprising of identification of at least one ir-lncRNA signature correlated with immune checkpoint expression.
Embodiment 8—The method of embodiment 7, wherein the ir-lncRNA signature comprises three lncRNAs.
Embodiment 9—The method of embodiment 7, wherein the ir-lncRNA signature comprises the top 20 differentially expressed ir-lncRNAs in ICR high versus ICR low breast tumors
Embodiment 10—The method of embodiment 7, wherein the ir-lncRNA signature comprises the top 20 ir-lncRNAs that are positively correlated with immune checkpoint expression.
Embodiment 11—The method of any preceding embodiment, wherein said ir-lncRNA signature comprises at least one of PCED1B-AS1, RP11-291B21.2 and AC092580.4.
Embodiment 12—The method of any preceding embodiment, further comprising development of a cancer treatment protocol for the patient.
Embodiment 13—The method of embodiment 12, further comprising administration of a cancer treatment comprising at least one of chemotherapy, radiation therapy, and immunotherapy.
The terms “a,” “an,” “the” and similar referents used in the context of describing the invention (especially in the context of the following claims) are to be construed to cover both the singular and the plural, unless otherwise indicated herein or clearly contradicted by context. Recitation of ranges of values herein is merely intended to serve as a shorthand method of referring individually to each separate value falling within the range. Unless otherwise indicated herein, each individual value is incorporated into the specification as if it were individually recited herein. All methods described herein can be performed in any suitable order unless otherwise indicated herein or otherwise clearly contradicted by context. The use of any and all examples, or exemplary language (e.g., “such as”) provided herein is intended merely to better illuminate the invention and does not pose a limitation on the scope of the invention otherwise claimed. No language in the specification should be construed as indicating any non-claimed element essential to the practice of the invention.
Groupings of alternative elements or embodiments of the invention disclosed herein are not to be construed as limitations. Each group member may be referred to and claimed individually or in any combination with other members of the group or other elements found herein. It is anticipated that one or more members of a group may be included in, or deleted from, a group for reasons of convenience and/or patentability. When any such inclusion or deletion occurs, the specification is deemed to contain the group as modified thus fulfilling the written description of all Markush groups used in the appended claims.
Certain embodiments of this invention are described herein, including the best mode known to the inventors for carrying out the invention. Of course, variations on these described embodiments will become apparent to those of ordinary skill in the art upon reading the foregoing description. The inventor expects skilled artisans to employ such variations as appropriate, and the inventors intend for the invention to be practiced otherwise than specifically described herein. Accordingly, this invention includes all modifications and equivalents of the subject matter recited in the claims appended hereto as permitted by applicable law. Moreover, any combination of the above-described elements in all possible variations thereof is encompassed by the invention unless otherwise indicated herein or otherwise clearly contradicted by context.
Specific embodiments disclosed herein may be further limited in the claims using consisting of or consisting essentially of language. When used in the claims, whether as filed or added per amendment, the transition term “consisting of” excludes any element, step, or ingredient not specified in the claims. The transition term “consisting essentially of” limits the scope of a claim to the specified materials or steps and those that do not materially affect the basic and novel characteristic(s). Embodiments of the invention so claimed are inherently or expressly described and enabled herein.
Furthermore, numerous references have been made to patents and printed publications throughout this specification. Each of the above-cited references and printed publications are individually incorporated herein by reference in their entirety.
In closing, it is to be understood that the embodiments of the invention disclosed herein are illustrative of the principles of the present invention. Other modifications that may be employed are within the scope of the invention. Thus, by way of example, but not of limitation, alternative configurations of the present invention may be utilized in accordance with the teachings herein. Accordingly, the present invention is not limited to that precisely as shown and described.
It should be understood that various changes and modifications to the presently preferred embodiments described herein will be apparent to those skilled in the art. Such changes and modifications can be made without departing from the spirit and scope of the present subject matter and without diminishing its intended advantages. It is therefore intended that such changes and modifications be covered by the appended claims.
This application claims the benefit of, and priority to, U.S. Provisional Patent Application Ser. No. 63/336,576, filed on Apr. 29, 2022, the entire disclosure of which is hereby incorporated by reference in its entirety.
| Number | Date | Country | |
|---|---|---|---|
| 63336576 | Apr 2022 | US |
