Molecular medicine hones therapeutic arts to science

Bioinformatic primer for clinical and translational science

The advent of high-throughput technologies has accelerated generation and expansion of genomic, transcriptomic, and proteomic data. Acquisition of high-dimensional datasets requires archival systems that permit efficiency of storage and retrieval, and so, multiple electronic repositories have been initiated and maintained to meet this demand. Bioinformatic science has evolved, from these intricate bodies of dynamically updated information and the tools to manage them, as a necessity to harness and decipher the inherent complexity of high-volume data. Large datasets are associated with a variable degree of stochastic noise that contributes to the balance of an ordered, multistable state with the capacity to evolve in response to stimulus, thus exhibiting a hallmark feature of biological criticality. In this context, the network theory has become an invaluable tool to map relationships that integrate discrete elements that collectively direct global function within a particular -omic category, and indeed, the prioritized focus on the functional whole of the genomic, transcriptomic, or proteomic strata over single molecules is a primary tenet of systems biology analyses. This new biology perspective allows inspection and prediction of disease conditions, not limited to a monogenic challenge, but as a combination of individualized molecular permutations acting in concert to effect a phenotypic outcome. Bioinformatic integration of multidimensional data within and between biological layers thus harbors the potential to identify unique biological signatures, providing an enabling platform for advances in clinical and translational science.

Strategies for therapeutic repair: The "R(3)" regenerative medicine paradigm

Beyond the palliative reach of today, medical therapies of tomorrow aim to treat the root cause of chronic degenerative diseases. Therapeutic repair encompasses the converging triad of rejuvenation, regeneration or replacement strategies that rely on self-healing processes, stem cell regeneration, and/or organ transplantation. Natural healing or rejuvenation exemplify inherent, baseline repair secured by tissue self-renewal and de novo cell biogenesis, particularly effective in organs with a high endogenous reparative capacity. Transplant medicine exploits the replacement strategy as a valuable option to recycle used parts and restore failing organ function by means of exogenous substitutes-it is, however, limited by donor shortage. Stem cell-based regeneration offers the next frontier of medical therapy through delivery of essentially unlimited pools of autologous or allogeneic, naive or modified, progenitor cells to achieve structural and functional repair. Translation into clinical applications requires the establishment of a regenerative medicine community of practice capable to bridge discovery with personalized treatment solutions. Indeed, this multidisciplinary specialized workforce will be capable to integrate the new science of embryology, immunology, and stem cell biology into bioinformatics and network medicine platforms, ensuring implementation of therapeutic repair strategies into individualized disease management algorithms.

Stem cell platforms for regenerative medicine

The pandemic of chronic degenerative diseases associated with aging demographics mandates development of effective approaches for tissue repair. As diverse stem cells directly contribute to innate healing, the capacity for de novo tissue reconstruction harbors a promising role for regenerative medicine. Indeed, a spectrum of natural stem cell sources ranging from embryonic to adult progenitors has been recently identified with unique characteristics for regeneration. The accessibility and applicability of the regenerative armamentarium has been further expanded with stem cells engineered by nuclear reprogramming. Through strategies of replacement to implant functional tissues, regeneration to transplant progenitor cells or rejuvenation to activate endogenous self-repair mechanisms, the overarching goal of regenerative medicine is to translate stem cell platforms into practice and achieve cures for diseases limited to palliative interventions. Harnessing the full potential of each platform will optimize matching stem cell-based biologics with the disease-specific niche environment of individual patients to maximize the quality of long-term management, while minimizing the needs for adjunctive therapy. Emerging discovery science with feedback from clinical translation is therefore poised to transform medicine offering safe and effective stem cell biotherapeutics to enable personalized solutions for incurable diseases.

Clinical pharmacology: a paradigm for individualized medicine

Individualized medicine provides a powerful engine revolutionizing the practice of clinical pharmacology, tailoring genetic and molecular profiles of patients to improve therapeutic specificity, reduce treatment variability and minimize adverse drug events. In that context, advances in individualized medicine have transformed the science of clinical pharmacology and therapeutics from drug discovery through identification of drugable targets, development through stratification of disease risk, regulation through identifying pathways mediating off-target effects and utilization through personalizing drug regimens. This revolution in fundamental and applied therapeutics has entrained an evolution in biology and medicine. Insights in the mechanistic basis of cell, tissue and organ function, and their interface with the environment are being translated to define disease risk, identify processes mediating disease susceptibility, target mechanism-based therapies, and tailor prevention and control paradigms, providing previously unanticipated opportunities for patient-specific disease management. The emerging field of individualized medicine is transforming the practice of clinical pharmacology, driving the leading edge of discovery from the laboratory bench to the evidence basis of practice in the clinic, extending to populations, to transform healthcare and create predictive, personalized and pre-emptive solutions for tailored patient-specific therapeutic strategies.

Induced pluripotent stem cells: advances to applications

Induced pluripotent stem cell (iPS) technology has enriched the armamentarium of regenerative medicine by introducing autologous pluripotent progenitor pools bioengineered from ordinary somatic tissue. Through nuclear reprogramming, patient-specific iPS cells have been derived and validated. Optimizing iPS-based methodology will ensure robust applications across discovery science, offering opportunities for the development of personalized diagnostics and targeted therapeutics. Here, we highlight the process of nuclear reprogramming of somatic tissues that, when forced to ectopically express stemness factors, are converted into bona fide pluripotent stem cells. Bioengineered stem cells acquire the genuine ability to generate replacement tissues for a wide-spectrum of diseased conditions, and have so far demonstrated therapeutic benefit upon transplantation in model systems of sickle cell anemia, Parkinson’s disease, hemophilia A, and ischemic heart disease. The field of regenerative medicine is therefore primed to adopt and incorporate iPS cell-based advancements as a next generation stem cell platforms.

A study of microRNAs in silico and in vivo: diagnostic and therapeutic applications in cancer

There is emerging evidence of the production in human tumors of abnormal levels of microRNAs (miRNAs), which have been assigned oncogenic and/or tumor-suppressor functions. While some miRNAs commonly exhibit altered amounts across tumors, more often, different tumor types produce unique patterns of miRNAs, related to their tissue of origin. The role of miRNAs in tumorigenesis underscores their value as mechanism-based therapeutic targets in cancer. Similarly, unique patterns of altered levels of miRNA production provide fingerprints that may serve as molecular biomarkers for tumor diagnosis, classification, prognosis of disease-specific outcomes and prediction of therapeutic responses.

Association of GUCY2C expression in lymph nodes with time to recurrence and disease-free survival in pN0 colorectal cancer

CONTEXT

The established relationship between lymph node metastasis and prognosis in colorectal cancer suggests that recurrence in 25% of patients with lymph nodes free of tumor cells by histopathology (pN0) reflects the presence of occult metastases. Guanylyl cyclase 2C (GUCY2C) is a marker expressed by colorectal tumors that could reveal occult metastases in lymph nodes and better estimate recurrence risk.

OBJECTIVE

To examine the association of occult lymph node metastases detected by quantifying GUCY2C messenger RNA, using the reverse transcriptase-polymerase chain reaction, with recurrence and survival in patients with colorectal cancer.

DESIGN, SETTING, AND PARTICIPANTS

Prospective study of 257 patients with pN0 colorectal cancer enrolled between March 2002 and June 2007 at 9 US and Canadian centers (7 academic medical centers and 2 community hospitals) provided 2570 fresh lymph nodes measuring 5 mm or larger for histopathology and GUCY2C messenger RNA analysis. Patients were followed up for a median of 24 months (range, 2-63 months) for disease recurrence or death.

MAIN OUTCOME MEASURES

Time to recurrence (primary outcome) and disease-free survival (secondary outcome) relative to expression of GUCY2C in lymph nodes.

RESULTS

Thirty-two patients (12.5%) had lymph nodes negative for GUCY2C (pN0 [mol-]), and all but 2 remained free of disease during follow-up (recurrence rate, 6.3%; 95% confidence interval [CI], 0.8%-20.8%). Conversely, 225 patients (87.5%) had lymph nodes positive for GUCY2C (pN0 [mol+]), and 47 developed recurrent disease (20.9%; 95% CI, 15.8%-26.8%) (P = .006). Multivariate analyses revealed that GUCY2C in lymph nodes was an independent marker of prognosis. Patients who were pN0 (mol+) exhibited earlier time to recurrence (adjusted hazard ratio, 4.66; 95% CI, 1.11-19.57; P = .04) and reduced disease-free survival (adjusted hazard ratio, 3.27; 95% CI, 1.15-9.29; P = .03).

CONCLUSION

Expression of GUCY2C in histologically negative lymph nodes appears to be independently associated with time to recurrence and disease-free survival in patients with pN0 colorectal cancer.