The QChip1 knowledgebase and microarray for precision medicine in Qatar.

Risk genes for Mendelian (single-gene) disorders (SGDs) are consistent across populations, but pathogenic risk variants that cause SGDs are typically population-private. The goal was to develop "QChip1," an inexpensive genotyping microarray to comprehensively screen newborns, couples, and patients for SGD risk variants in Qatar, a small nation on the Arabian Peninsula with a high degree of consanguinity. Over 108 variants in 8445 Qatari were identified for inclusion in a genotyping array containing 165,695 probes for 83,542 known and potentially pathogenic variants in 3438 SGDs. QChip1 had a concordance with whole-genome sequencing of 99.1%. Testing of QChip1 with 2707 Qatari genomes identified 32,674 risk variants, an average of 134 pathogenic alleles per Qatari genome. The most common pathogenic variants were those causing homocystinuria (1.12% risk allele frequency), and Stargardt disease (2.07%). The majority (85%) of Qatari SGD pathogenic variants were not present in Western populations such as European American, South Asian American, and African American in New York City and European and Afro-Caribbean in Puerto Rico; and only 50% were observed in a broad collection of data across the Greater Middle East including Kuwait, Iran, and United Arab Emirates. This study demonstrates the feasibility of developing accurate screening tools to identify SGD risk variants in understudied populations, and the need for ancestry-specific SGD screening tools.

Diabetic Kidney Disease: Past and Present.

Diabetes mellitus (DM) afflicting humans has been recognized as a disease for >3000 years. However, very little was known about its etiology and pathogenesis until about a century ago when increasing knowledge about anatomy and physiology of the human body gradually led to our understanding that the hormone insulin produced by the Islets of Langerhans in the pancreas plays a crucial role in the metabolism of glucose and maintaining the blood sugar level within a normal range. DM is caused by inadequate insulin production (type 1) or insulin resistance (type 2). For thousands of years, DM has been considered as a disease of the kidney; however, with the understanding of the pathogenesis of DM, it became clear that diabetic kidney disease (DKD) is a complication and not a cause of DM. DKD is associated with increased matrix expansion that manifests morphologically as a diffuse or nodular expansion of the mesangium and diffuse thickening of the glomerular and tubular basement membranes. Hyperglycemia plays a crucial role in the development of pathologic changes within the kidney. Once established, DKD usually undergoes a slow but relentless progression to end-stage renal disease. However, recent studies have shown that its progression can be slowed or even reversed by strict control of hyperglycemia. Morphologically, DKD may resemble several other glomerular diseases that must be ruled out before a definitive diagnosis. Patients with DM may also develop nondiabetic glomerular or interstitial diseases with or without DKD. The findings in nephrectomy specimens and the differential diagnoses are presented in detail.

Classification of Endometrial Carcinoma: New Perspectives Beyond Morphology.

Endometrial carcinoma has been traditionally divided into type 1 or endometrioid type that is usually moderate to well differentiated and type 2 that is usually poorly differentiated with high histologic grade and aggressive clinical behavior. However, interobserver diagnostic agreement is suboptimal, particularly among the high-grade histotypes. Furthermore, recent data indicate that this histotype assignment does not independently correlate with survival. In recent years, there has been remarkable progress in our understanding of the molecular basis of endometrial carcinoma and extensive molecular studies have been performed under The Cancer Genome Atlas Program (TCGA) leading to molecular classification of endometrial carcinoma that has been shown to be significantly prognostic. This classification system divides the tumors into 4 subgroups namely, polymerase ε exonuclease (POLE) ultramutated, hypermutated microsatellite instability, copy number low, and copy number high (serous-like). Carcinomas with POLE domain hotspot mutations are highly prognostically favorable; those with copy number alterations and TP53 mutations are highly aggressive; and microsatellite unstable and "copy number low" endometrioid are associated with intermediate prognoses. The TCGA applied methods that are too costly and cumbersome for widespread implementation into routine clinical practice. Several other groups have attempted to identify these categories by using immunohistochemical biomarkers rather than molecular studies. Immunohistochemical biomarkers have been used successfully to identify all the subgroups except for POLE ultramutated, which requires sequencing for proper categorization. It is hoped that future studies will identify a suitable biomarker for POLE mutation so that this classification can be routinely used in all medical centers.

Urothelial Carcinoma In Situ (CIS): New Insights.

Urothelial carcinoma in situ (CIS) is a high-grade noninvasive malignancy with a high tendency of progression. Although it is typically grouped with other nonmuscle invasive bladder cancers, its higher grade and aggressiveness make it a unique clinical entity. Urothelial CIS is histologically characterized by replacement of the urothelium by cells which fulfill the morphologic criteria of malignancy including nuclear pleomorphism, hyperchromasia, prominent nucleoli, and increased numbers of normal and abnormal mitoses. Urothelial CIS may be categorized as primary when it is not associated with any past or present urothelial carcinoma. It is termed as secondary when there is concomitant or previous urothelial carcinoma in the patient. In recent years detailed molecular studies have provided valuable data for intrinsic molecular subclassification of urothelial carcinoma into 2 broad categories namely luminal and basal types with significant implications for prognosis and therapy. Similar studies on urothelial CIS are limited but have provided crucial insight into the molecular basis of CIS. These studies have revealed that urothelial CIS may also be divided into luminal and basal subtypes, but luminal subtype is much more common. It has also been shown that in many cases, luminal type of urothelial CIS may undergo a class switch to basal type during progression to an invasive carcinoma. Additional studies may be required to confirm and further elaborate these findings.

Paget's "Seed and Soil" Theory of Cancer Metastasis: An Idea Whose Time has Come.

The concept that the pattern of metastatic spread of cancer is not random and that cancer cells exhibit preferences when metastasizing to organs, dates back to 1889 when Steven Paget published his "seed and soil" hypothesis. He proposed that the spread of tumor cells is governed by interaction and cooperation between the cancer cells (seed) and the host organ (soil). Extensive studies during the last several decades have provided a better understanding of the process of metastatic spread of cancer and several stages such as intravasation, extravasation, tumor latency, and development of micrometastasis and macrometastasis have been defined. Furthermore, recent studies have shown that the target organs may be prepared for metastatic deposits by the development of premetastatic niches. This specialized microenvironment is involved in promoting tumor cell homing, colonization, and subsequent growth at the target organ. The premetastatic niche consists of accumulation of aberrant immune cells and extracellular matrix proteins in target organs. The primary tumor plays a key role in the development of premetastatic niches by producing tumor-derived soluble factors which mobilize bone marrow-derived hematopoietic cells to the premetastatic niche. Exosomes-derived from the primary tumor also contribute to cancer-favorable microenvironment in the premetastatic niches. These changes prime the initially healthy organ microenvironment and render it amenable for subsequent metastatic cell colonization.